Taxonomy of Protista

A modern non-hierarchical interpretation of the phylogeny of protists

A protist (/ˈproʊtɪst/) is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor;^{[lower-alpha 1]} but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues".^[1]^{[lower-alpha 2]} In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista (containing the chromalveolate, rhizarian and hacrobian groups) and Protozoa (containing excavates and all protists more closely related to animals and fungi).^[2]

The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.

Key to symbols used:

(P) = Paraphyletic group.

† = Extinct group.

? = Group of uncertain taxonomic position.

* = Group lacking molecular data.

Current classification

This article largely follows the efforts of the scientific community and the International Society of Protistologists to revise the taxonomy of protists in a manner that reflects their phylogeny and evolution, striving away from the use of historical paraphyletic taxa and relying exclusively on clades as the basis of the classification. The reference used for the general arrangement of groups is the publication Revisions to the Classification, Nomenclature and Diversity of Eukaryotes, published in 2019 by researcher Sina Adl and coauthors.^[3] Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds,^[4] glaucophyte algae,^[5] arcellinid testate amoebae^[6] and planktonic foraminifera.^[7]

The following cladogram shows the relationships between the major groups of protists, as well as the kingdoms of animals, plants and fungi, according to the most recent phylogenetic analyses.^[8]^[9]^[10]^[11]^[12]

	Stramenopiles

	Alveolata

CAM

	Cryptista

	Microheliella

Archaeplastida (Kingdom Plantae s.l.)

	Heterolobosea

	Euglenozoa

	Fungi

	Cristidiscoidea

	Choanoflagellata

	Metazoa (Kingdom Animalia)

Choanozoa (P)
sensu Cavalier-Smith

Excavates (P)

Amorphea Adl et al. 2012

Obazoa Brown et al. 2013

Incertae sedis Obazoa:

Apusomonadida Karpov & Mylnikov 1989 [Apusomonadidae Karpov & Mylnikov 1989; Thecomonadea Cavalier-Smith 1993 em. 2013; Apusozoa Cavalier-Smith 1997 em. 2013 pro parte]. Amastigomonas, Apusomonas, Chelonemonas, Manchomonas, Multimonas, Podomonas, Thecamonas, Catacumbia, Cavaliersmithia, Karpovia, Singekia.^[13]
Breviatea Cavalier-Smith 2004 [Breviatida Cavalier-Smith 2004; Breviatidae Cavalier-Smith 2013; Apusozoa Cavalier-Smith 1997 em. 2013 pro parte]. Breviata, Lenisia, Pygsuia, Subulatomonas.

Opisthokonta Cavalier-Smith 1987, emend. Adl et al. 2005

Nucletmycea Brown et al. 2009 [Holomycota Liu et al. 2009]
- Rotosphaerida Rainer 1968 [Cristidiscoidida Page 1987, Cavalier-Smith 1993, 1998; Nucleariidae Patterson 1983, 1999]. Fonticula, Nuclearia, Parvularia, Pompholyxophrys, Lithocolla, ?Vampyrellidium*, ?Elaeorhanis*, ?Pinaciophora*, ?Rabdiophrys*, ?Rabdiaster*, ?Thomseniophora*.^[14]
- Fungi R.T. Moore 1980. Excluded from protists.
Holozoa Lang et al. 2002. Incertae sedis: Tunicaraptor Tikhonenkov, Mikhailov, Hehenberger, Karpov, Prokina, Esaulov, Belyakova, Mazei, Mylnikov, Aleoshin & Keeling 2020,^[11] †Bicellum brasieri Strother & Wellman 2021.^[15]
- Ichthyosporea^{[lower-alpha 3]} Cavalier-Smith 1998 [Mesomycetozoea Mendoza et al. 2002]
  - Dermocystida Cavalier-Smith 1998 [Rhinosporidaceae Mendoza et al. 2001]. Amphibiocystidium, Amphibiothecum, Chromosphaera, Dermocystidium, Rhinosporidium, Sphaerothecum.
  - Ichthyophonida Cavalier-Smith 1998 [Ichthyophonae Mendoza et al. 2001; Amoebidiidae Reeves 2003]. Abeoforma, Amoebidium, Anurofeca, Astreptonema, Caullerya, Creolimax, Eccrinidus, Enterobryus, Enteropogon, Ichthyophonus, Palavascia, Pseudoperkinsus, Psorospermium, Sphaeroforma.
- Pluriformea^{[lower-alpha 3]} Hehenberger et al. 2017
  - Corallochytrium limacisporium Raghu-Kumar 1987
  - Syssomonas multiformis^{[lower-alpha 3]} Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017
- Filasterea Shalchian-Tabrizi et al. 2008. Capsaspora, Ministeria, Pigoraptor, Txikispora.^[16]
- Choanozoa Brunet & King 2017 [Choanozoa Cavalier-Smith et al. 1991 (P)]^{[lower-alpha 4]}
  - Choanoflagellata Kent 1880–1882 [Craspedomonadina Stein 1878; Craspedomonadaceae Senn 1900; Craspedophyceae Chadefaud 1960; Craspédomonadophycidées Bourrelly 1968; Craspedomonadophyceae Hibberd 1976; Choanomonadea Krylov et al. 1980; Choanoflagelliida Lee, Hutner & Bovee 1985; Choanoflagellatea Cavalier-Smith 1997 emend. Cavalier-Smith 1998; Choanomonada Adl et al. 2005].
    - Craspedida Cavalier-Smith 1997, emend. Nitsche et al. 2011
      - Salpingoecidae Kent 1880–1882, emend. sensu Nitsche et al. 2011. Astrosiga, Aulomonas, Choanoeca, Cladospongia, Codonocladium, Codonosigopsis, Codosiga [Codonosiga], Desmarella [Codonodesmus; Kentrosiga], Dicraspedella, Diploeca, Diplosiga, Diplosigopsis, Hartaetosiga, Kentia, Lagenoeca, Microstomoeca, Monosiga, Mylnosiga, Pachysoeca, Proterospongia, Salpingoeca, Salpingorhiza, Sphaeroeca, Stagondoeca, Stelexomonas, Stylochromonas.
    - Acanthoecida Cavalier-Smith 1997, emend. Nitsche et al. 2011
      - Acanthoecidae Norris 1965, emend. sensu Nitsche et al. 2011. Acanthoeca, Enibas,^[17] Helgoeca, Polyoeca, Savillea.
      - Stephanoecidae Leadbeater 2011. Acanthocorbis, Amoenoscopa, Apheloecion, Bicosta, Calliacantha, Calotheca, Campanoeca, Campyloacantha, Conion, Cosmoeca, Crinolina, Crucispina, Diaphanoeca, Didymoeca, Kakoeca, Monocosta, Nannoeca, Parvicorbicula, Platypleura, Pleurasiga, Polyfibula, Saepicula, Saroeca, Spinoeca, Spiraloecion, Stephanacantha, Stephanoeca, Syndetophyllum.
  - Metazoa Haeckel 1874, emend. Adl et al. 2005 [Animalia Linnaeus 1758; Eumetazoa Bütschli 1910]. Excluded from protists.

Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998

Phylogeny of Amoebozoa^[18]

Divosa

	Archamoebea

	Eumycetozoa

Incertae sedis Amoebozoa: Belonocystis, Boveella, Biomyxa, Corallomyxa, Gibbodiscus, Hartmannia, Malamoeba, Malpighamoeba, Microcorycia, Microglomus, Oscillosignum, Parmulina, Penardochlamys, Pseudothecamoeba, Rhabdamoeba, Schoutedamoeba, Stereomyxa, Subulamoeba, Thecochaos, Triaenamoeba, Unda, Zonomyxa.^[3]

Tubulinea Smirnov et al. 2005

Corycida Kang et al. 2017.^[19] Amphizonella, Diplochlamys, Trichosphaerium (=Atrichosa), ?Microcorycia, ?Parmulina, ?Penardochlamys, ?Zonomyxa.^{[lower-alpha 5]}
Echinamoebida Cavalier-Smith 2004.
- Echinamoebidae Page 1975. Echinamoeba, Micriamoeba.
- Vermamoebidae Cavalier-Smith & Smirnov 2011. Vermamoeba.
Elardia Kang et al. 2017^[19]
- Leptomyxida Pussard & Pons 1976 sensu Page 1987
  - Leptomyxidae Pussard & Pons 1976. Leptomyxa.
  - Rhizamoebidae Smirnov et al. 2016. Rhizamoeba.^[20]
  - Flabellulidae Bovee 1970. Flabellula [incl. Paraflabellula].
  - Gephyramoebidae Pussard & Pons 1976. Gephyramoeba.^[20]
- Arcellinida Kent 1880. Incertae sedis genera: Acipyxis, Apolimia, Argynnia, Armipyxis, Conicocassis, Cornuapyxis, Ellipsopyxella, Ellipsopyxis, Erugomicula, Frenopyxis, Geamphorella, Geoplagiopyxis, Geopyxella, Hoogenraadia, Jungia, Lagenodifflugia, Lamptopyxis, Lamptoquadrula, Leptochlamys, Maghrebia, Meisterfeldia, Microquadrula, Nabranella, Oopyxis, Paracentropyxis, Paraquadrula, Pentagonia, Physochila, Planhoogenraadia, Pomoriella, Pontigulasia, Prantlitina,^[21] Proplagiopyxis, Protoplagiopyxis, Protocucurbitella, Pseudawerintzewia, Pseudonebela, Schoenbornia, Sexangularia, Suiadifflugia, Trigonopyxis, Wailesella.^[6]
  - Phryganellina Bovee 1985
    - Phryganellidae Jung 1942. Phryganella.
    - Cryptodifflugiidae Jung 1942. Cryptodifflugia.^[22]
  - Organoconcha Lahr et al. 2019
    - Microchlamyiidae Ogden 1985. Microchlamys, Spumochlamys, Pyxidicula.
  - Glutinoconcha Lahr et al. 2019
    - Volnustoma Lahr et al. 2019
      - Heleoperidae Jung 1942. Heleopera.
    - Hyalospheniformes Lahr et al. 2019
      - Hyalospheniidae Schultze 1877 emend. Kosakyan et al. 2012. Alabasta, Alocodera, Apodera, Certesella, Cornutheca, Gibbocarina, Hyalosphenia, Longinebela, Mrabella, Nebela, Padaungiella, Planocarina, Porosia, Quadrulella.
    - Excentrosoma Lahr et al. 2019
      - Centropyxidae Jung 1942 [includes Plagiopyxidae]. Awerinzewia, Bullinularia, Centropyxis, Golemanskia,^[6] Plagiopyxis.
    - Cylindrothecina González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022
      - Cylindrifflugiidae González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022.^[6] Cylindrifflugia.
    - Longithecina Lahr et al. 2019
      - Difflugiidae Wallich 1864. Difflugia, Zivkovicia.
      - Lesquereusiidae Jung 1942. Lesquereusia.
    - Sphaerothecina Kosakyan et al. 2016
      - Arcellidae Ehrenberg 1843. Arcella, Galeripora.
      - Netzeliidae Kosakyan et al. 2016. Cucurbitella, Cyclopyxis, Netzelia
- Euamoebida Lepşi 1960 sensu Smirnov et al. 2011^[23]
  - Amoebina Cavalier-Smith 2016
    - Amoebidae Ehrenberg 1838 Page 1987. Amoeba, Chaos, Polychaos, Parachaos, Trichamoeba, Deuteramoeba, Hydramoeba
    - Hartmannellidae Volkonsky 1931. Cashia, Copromyxa, Copromyxella, Glaeseria, Hartmannella, Ptolemeba, Saccamoeba
  - Nolandina Cavalier-Smith 2016^[23]
    - Nolandellidae Cavalier-Smith 2011, Lahr & Katz 2011. Nolandella.

Evosea Kang et al. 2017

Variosea^{[lower-alpha 6]} Cavalier-Smith 2004
- Angulamoeba Berney, Bass & Geisen 2015
- Arboramoeba Berney, Bass & Geisen 2015
- Darbyshirella Berney, Bass & Geisen 2015
- Dictyamoeba Berney, Bass & Geisen 2015
- Ischnamoeba Berney, Bass & Geisen 2015
- Heliamoeba Berney, Bass & Geisen 2015
- Filamoeba Page 1967
- Phalansterium Cienkowski 1870.
- Flamellidae Cavalier-Smith 2016. Flamella, Telaepolella.
- Protosteliida Olive & Stoianovitch 1966, sensu Shadwick & Spiegel in Adl et al. 2012. Protostelium [incl. Planoprotostelium].
- Fractovitellida Lahr et al. 2011, sensu Kang et al. 2017
  - Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008. Acramoeba.
  - Schizoplasmodiidae Shadwick & Spiegel in Adl et al. 2012. Ceratiomyxella, Nematostelium, Schizoplasmodium.
  - Soliformoviidae Lahr & Katz 2011. Soliformovum, Grellamoeba
- Cavosteliida Shadwick & Spiegel in Adl et al. 2012. Cavostelium, Schizoplasmodiopsis, Tychosporium.
- Holomastigida Lauterborn 1895. Artodiscus, Multicilia.
Eumycetozoa Zopf 1884 sensu Kang et al. 2017 [Mycetozoa de Bary 1859 ex Rostafinski 1873; Macromycetozoa Fiore-Donno 2010]
- Dictyostelia Lister 1909 sensu Sheikh et al. 2018 [Dictyosteliomycetes Doweld 2001]. Acytostelium, Cavenderia, Coremiostelium, Dictyostelium, Heterostelium, Polysphondylium, Raperostelium, Rostrostelium, Speleostelium, Tieghemostelium, Synstelium, ?Coenonia.
- Protosporangiida Shadwick & Spiegel in Adl et al. 2012 [Ceratiomyxea Leontyev, Stephenson, Novozhilov & Shchepin 2019; Ceratiomyxomycetes D. Hawksw., B. Sutton & Ainsw. 2019]^[4]
  - Ceratiomyxa Schroeter 1889
  - Protosporangiidae Spiegel in Adl et al. 2012. Clastostelium, Protosporangium.
- Myxogastria Macbride 1899 [Myxogastrea Cavalier-Smith 1993; Myxomycetes Link 1833, sensu Haeckel 1866]
  - Lucisporomycetidae [Lucisporinia Leontyev, Stephenson, Novozhilov & Shchepin 2019;^[4] Lucisporidia Cavalier-Smith 2013]. Incertae sedis genera: Arcyriatella, Calonema, Minakatella, Trichioides.
    - Cribariidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
      - Cribariales T. Macbr. 1922
        Cribariaceae Corda 1838. Cribaria, Lindbladia, Licaethalium.
    - Trichiidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
      - Reticulariales Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        Reticulariaceae Chevall. 1842. Alwisia, Lycogala, Reticularia, Tubifera.
      - Liceales E. Jahn 1928
        Liceaceae Chevall. 1826. Licea, Listerella.
      - Trichiales T. Macbr. 1922
        Dianemataceae T. Macbr. 1922. Calomyxa, Dianema, Dictydiaethalium, Prototrichia.
        
        Trichiaceae Chevall. 1826 sensu Martin & Alexopoulos 1969. Hemitrichia [incl. Trichia decipiens], Arcyria [incl. Arcyodes], Perichaena, Trichia [incl. Cornuvia, Metatrichia, Oligonema].
  - Columellomycetidae [Collumellinia Leontyev, Stephenson, Novozhilov & Shchepin 2019;^[4] Columellidia Cavalier-Smith 2015]. Incertae sedis genera: Diachea, Echinosteliopsis, Leptoderma, Paradiachea, Protophysarum, Trabrooksia, Willkommlangea.
    - Echinosteliidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
      - Echinosteliales G. W. Martin 1961
        Echinosteliaceae Rostaf. ex Cooke 1877. Barbeyella, Echinostelium [incl. Semimorula].
    - Stemonitidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
      - Clastodermatales Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        Clastodermataceae Alexop. & T.E. Brooks 1971. Clastoderma.
      - Meridermatales Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        Meridermataceae Leontyev, Stephenson, Novozhilov & Shchepin 2019. Meriderma.
      - Stemonitidales T. Macbr. 1922 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019
        Stemonitidaceae Fr. 1829 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Macbrideola, Stemonitis, Symphytocarpus.
        
        Amaurochaetaceae Rostaf. ex Cooke 1877 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Comatricha, Stemonaria, Stemonitopsis, Amaurochaete, Brefeldia, Enerthenema, Paradiacheopsis.
      - Physarales T. Macbr. 1922
        Tasmaniomyxa umbilicata Lloyd et al. 2023^[24]
        
        Lamprodermataceae T. Macbr. 1899 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Lamproderma [incl. Dichaeopsis, Colloderma, Elaeomyxa], ?Collaria.
        
        Didymiaceae Rostaf. ex Cooke 1877 – Diderma, Didymium, Lepidoderma, Mucilago.
        
        Physaraceae Chevall. 1826. Craterium, Leocarpus, Fuligo, Physarum, Physarella, Physarina, Kelleromyxa, Badhamia.
Cutosea Cavalier-Smith 2016 [Squamocutida Cavalier-Smith 2016]
- Squamamoebidae Cavalier-Smith 2016. Armaparvus, Squamamoeba.
- Sapocribridae Cavalier-Smith 2016. Sapocribrum.
Archamoebea Cavalier-Smith 1983, sensu Cavalier-Smith 2004
- Tricholimacidae Cavalier-Smith 2012. Tricholimax.
- Entamoebidae Chatton 1925. Entamoeba.
- Rhizomastixidae Ptáčková et al. 2013. Rhizomastix.
- Mastigamoebida Frenzel 1897, sensu Cavalier-Smith 2013.^{[lower-alpha 7]} Endamoeba, Endolymax, Iodamoeba, Mastigamoeba, Mastigina.
- Pelobiontida Page 1976, sensu Cavalier-Smith 2013 [Pelomyxidae Schulze 1877]. Mastigella, Pelomyxa

Discosea Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011

Flabellinia Smirnov et al. 2005
- Dermamoebida Cavalier-Smith 2004
  - Dermamoebidae Cavalier-Smith & Smirnov 2011. Dermamoeba, Paradermamoeba, ?Mycamoeba,^{[lower-alpha 8]} Coronamoeba.^[26]
  - Mayorellidae Schaeffer 1926. Mayorella.
- Thecamoebida^{[lower-alpha 7]} Schaeffer 1926, sensu Smirnov & Cavalier-Smith 2011. Sappinia, Stenamoeba, Stratorugosa,^[27] Thecamoeba, Thecochaos.^[28]
- Dactylopodida^{[lower-alpha 7]} Smirnov et al. 2005 sensu Kang et al. 2017. Cunea, ?Janickina,* Korotnevella, Neoparamoeba, Paramoeba, Pseudoparamoeba, Vexillifera.
- Vannellida Smirnov et al. 2005 [Vannellidae Bovee 1979]. Clydonella, Lingulamoeba, Paravannella, Pessonella*,^{[lower-alpha 9]} Ripella, Vannella.
Stygamoebida^{[lower-alpha 10]} Smirnov & Cavalier-Smith in Smirnov et al. 2011 (P). Stygamoeba, Vermistella.
Centramoebia Cavalier-Smith et al. 2016^[23]
- Acanthopodida^{[lower-alpha 7]} Page 1976 [Centramoebida Rogerson & Patterson 2002, sensu Tice et al. 2016^[29]]. Acanthamoeba, Balamuthia, Luapeleamoeba, Protacanthamoeba, Dracoamoeba, Vacuolamoeba.
- Himatismenida^{[lower-alpha 7]} Page 1987. Cochliopodium, Ovalopodium, Parvamoeba.
- Pellitida^{[lower-alpha 7]} Smirnov & Cavalier-Smith 2011, sensu Kang et al. 2017. Endostelium, Gocevia, Paragocevia*, Pellita.

Diaphoretickes Adl et al. 2012

Microheliella maris^{[lower-alpha 11]} Cavalier-Smith 2012
Telonemia^{[lower-alpha 12]} Shalchian-Tabrizi 2006 [Telonemidae Cavalier-Smith 1993]. Arpakorses,^[30] Lateronema, Telonema.
Provora Tikhonenkov et al. 2022^[10]
- Nibbleridia Tikhonenkov et al. 2022. Nibbleromonas, Ubysseya.
- Nebulidia Tikhonenkov et al. 2022. Nebulomonas, Ancoracysta.

Archaeplastida Adl et al. 2005

Glaucophyta Skuja 1954 [Glaucocystaceae West 1904; Glaucocystophyta Kies and Kremer 1986].^[5] Incertae sedis Glaucophyta: ?Archaeopsis, ?Chalarodora, ?Glaucocystopsis, ?Peliaina, ?Strobilomonas.
- Cyanophorales Kies & Kremer 2006. Cyanophora.
- Glaucocystales Bessey 1907. Glaucocystis.
- Gloeochaetales Bessey 1907. Cyanoptyche, Gloeochaete.
Picozoa Seenivasan et al. 2013 [Picobiliphytes Not et al. 2007]. Picomonas.^{[lower-alpha 13]}
Rhodelphidia Gawryluk et al. 2019. Rhodelphis.^[32]
Rhodophyceae Thuret 1855, emend. Rabenhorst 1863 [Rhodophyta Wettstein 1901; Rhodoplantae Saunders and Hommersand 2004 emend. Adl et al. 2005]
Chloroplastida Adl et al. 2005 [Viridiplantae Cavalier-Smith 1981; Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004; Chlorobiota Kendrick and Crane 1997]

SAR Burki et al. 2008, emend. Adl et al. 2012

Stramenopiles Patterson 1989, emend. Adl et al. 2005

? Environmental clades MAST-21, MAST-25 Massana et al. 2014
? Platysulcus tardus Shiratori, Nakayama & Ishida 2015
? Kaonashia insperata Weston, Eglit & Simpson 2023^[33]
Bigyra Cavalier-Smith 1998, emend. 2006
- Opalozoa Cavalier Smith 1991, emend. 2006. Incertae sedis: Cantina, Rictus, environmental clades MAST-16, MAST-22 and MAST-24 Massana et al. 2014.
  - Placidozoa Cavalier-Smith 2013
    - Placididea Moriya, Nakayama & Inouye 2002. Allegra, Haloplacidia, Pendulomonas, Placidia, Placilonga, Suigetsumonas, Wobblia.^[34]
    - Nanomonadea Cavalier-Smith 2012 [clade MAST-3]. Incisomonas, Solenicola.
    - Opalomonadea Cavalier-Smith 2013 [clade MAST-12]. No described species.
    - Opalinata Wenyon 1926, emend. Cavalier-Smith 1997 [Slopalinida Patterson 1985]
      - Proteromonadea Grassé 1952. Karotomorpha, Proteromonas.
      - Opalinea Wenyon 1926. Cepedea, Opalina, Protoopalina, Protozelleriella, Zelleriella.
      - Blastocystis Alexeieff 1911
  - Bicosoecida Grassé 1926, emend. Karpov 1998. Adriamonas, Anoeca, Bicosoeca, Caecitellus, Cafeteria, Cafileria,^[35] Cyathobodo, Filos, Halocafeteria, Nanum, Paramonas, Pseudobodo, Pseudodendromonas, Otto, Regin.^[36]
- Sagenista Cavalier-Smith 1995. Incertae sedis: environmental clades MAST-4, MAST-7, MAST-8, MAST-9, MAST-10, MAST-11 and MAST-20 Massana et al. 2014.
  - Labyrinthulomycetes Dick 2001
    - Amphitremida Poche 1913, emend. Gomaa et al. 2003. Amphitrema, Archerella, Diplophrys, Paramphitrema.
    - Amphifilida Cavalier-Smith 2012. Amphifila, Fibrophrys, Sorodiplophrys.
    - Oblongichytrida Bennett et al. 2017. Oblongichytrium.
    - Labyrinthulida Doffein 1901. Aplanochytrium, Labyrinthula, Stellarchytrium.
    - Thraustochytrida Sparrow 1943. Althornia, Aurantiochytrium, Botryochytrium, Japanochytrium, Monorhizochytrium, Parietichytrium, Phycophthorum,^[37] Schizochytrium, Sicyoidochytrium, Thraustochytrium, Ulkenia.
  - Pseudophyllomitidae Shiratori et al. 2016 [clade MAST-6].^[38] Pseudophyllomitus.
Gyrista Cavalier-Smith 1998. Incertae sedis: environmental clades MAST-1, MAST-2 and MAST-23 Massana et al. 2014.
- Bigyromonadea Cavalier-Smith 1998
  - Developea Karpov & Aleoshin 2016. Developayella, Develorapax.
  - Pirsoniales Cavalier-Smith 1998, emend. 2006. Pirsonia.
- Pseudofungi Cavalier-Smith 1986 [Heterokontimycotina M.W. Dick 1976].
  - Hyphochytriales Sparrow 1960. Anisolpidium, Canteriomyces.
    - Anisolpidiaceae Karling 1943, emend. Dick 2001
    - Hyphochytridiomycetaceae Fischer 1892, emend. Karling 1939. Hyphochytrium.
    - Rhizidiomycetaceae Karling 1943. Latrostium, Rhizidiomyces, Rhizidiomycopsis.
  - Oomycetes Winter 1897, emend. Dick 1976 [Peronosporomycetes Dick 2001]. Incertae sedis genera: Atkinsiella, Ciliomyces, Crypticola, Ectrogella, Eurychasma, Halodaphnea, Haliphthoros, Haptoglossa, Lagena, Lagenisma, Olpidiopsis, Pontisma, Pythiella, Rozellopsis, Sirolpidium.
    - Saprolegnialean lineage Lara in Adl et al. 2019. Achlya, Aphanomyces, Aplanopsis, Apodachlya, Aquastella, Geolegnia, Leptomitus, Newbya, Pythiopsis, Protoachlya, Salisapilia, Saprolegnia, Thraustotheca.
    - Peronosporalean lineage Lara in Adl et al. 2019. Albugo, Bremia, Chlamydomyzium, Halophytopthora, Hyaloperonospora, Lagenidium, Myzocytiopsis, Peronospora, Plasmopara, Pythium, Pseudoperonospora, Phytophthora, Phytopythium, Pustula.
- Ochrophyta Cavalier-Smith 1986, emend. Cavalier-Smith & Chao 1996
  - Chrysista Cavalier-Smith 1986. Incertae sedis: environmental lineages MOCH-3 and MOCH-5 Massana et al. 2014, Chrysowaernella, Aurearena.
    - SII clade
      - Olisthodiscophyceae Barcytė, Eikrem & M. Eliáš 2021.^[39] Olisthodiscus.
      - Pinguiophyceae Kawachi et al. 2003. Glossomastix, Phaeomonas, Pinguiochrysis, Pinguiococcus, Polypodochrysis.
      - Limnistia Cavalier-Smith 1996 emend. 2006
        Chrysophyceae Pascher 1914. Incertae sedis: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion, Phaeoplaca.
        Chromulinales Pascher 1910. Chromulina, Chrysomonas.
        
        Hibberdiales Andersen 1989. Hibberdia.
        
        Ochromonadales Pascher 1910. Spumella, Pedospumella, Ochromonas.
        
        Paraphysomonadida Scoble & Cavalier-Smith 2014. Paraphysomonas.
        
        Synurales Andersen 1987. Chrysodidymus, Mallomonas, Synura, Tesselaria.
        
        Eustigmatophyceae Hibberd & Leedale 1971^[40]
        Eustigmatales Hibberd 1981
        Paraeustigmatos Fawley, Nemcová, & Fawley 2019
        
        Eustigmataceae Hibberd 1981. ?Ellipsoidion, Chlorobotrys, Eustigmatos, Pseudocharaciopsis, Vischeria.
        
        Monodopsidaceae Hibberd 1981. Microchloropsis, Monodopsis, Nannochloropsis, Pseudotetraedriella.
        
        Neomonodaceae Amaral et al. 2020. ?Botryochloropsis, Characiopsella, Munda, Neomonodus, Pseudellipsoidion.
        
        Goniochloridales Fawley, Elias & Fawley 2013. Goniochloris, Pseudostaurastrum, Tetraedriella, Trachydiscus, Vacuoliviride.
        
        Picophagea Cavalier-Smith 2006 emend. 2017^[41] [Synchromophyceae S.Horn & C.Wilhelm 2007]. Chlamydomyxa, Chrysopodocystis, Guanochroma, Leukarachnion, Picophagus, Synchroma.
    - SI clade
      - Raphidomonadea Chadefaud 1950 ex Silva 1980
        Raphidophycidae Cavalier-Smith 2013 [Chattonellales Throndsen in Tomas 1993 emend. Yamaguchi, Nakayama, Murakami & Inouye 2010; Vacuolariales Shameel, 2001]. Chattonella, Fibrocapsa, Goniostomum, Haramonas, Heterosigma, Merotricha, Vacuolaria.
        
        Raphopoda Cavalier-Smith 2013
        Commatiida Cavalier-Smith 1997 [Commatiidae Cavalier-Smith 2013]. Commation.
        
        Actinophryida^{[lower-alpha 14]} Claus 1874, emend. Hartmann 1926
        Actinosphaerina Cavalier-Smith 2013 [Actinosphaeriidae Cavalier-Smith 2013]. Actinosphaerium.
        
        Actinophryina Cavalier-Smith 2013
        Actinophryidae Dujardin 1841. Actinophrys.
        
        Helioraphidae Cavalier-Smith 2013. Heliorapha.
      - PX clade
        Chrysomerophyceae Cavalier-Smith 1995. Antarctosaccion, Chrysomeris, Chrysowaernella, Giraudyopsis, Rhamnochrysis, Tetrasporopsis.
        
        Chrysoparadoxophyceae Wetherbee et al. 2019.^[43] Chrysoparadoxa.
        
        Phaeophyceae Hansgirg 1886 [Kjellman 1891; Pfitzer 1894]
        Ascoseirales Petrov 1964. Ascoseira.
        
        Desmarestiales Setchell & Gardner 1925. Arthrocladia, Desmarestia (P), Himantothallus, Phaeurus.
        
        Dictyotales Bory de Saint-Vincent 1828. Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
        
        Discosporangiales Kawai et al. 2007. Choristocarpus, Discosporangium.
        
        Ectocarpales Bessey 1907, emend. Silva & Reviers 2000. Adenocystis, Acinetospora, Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
        
        Fucales Bory de Saint-Vincent 1927. Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira, Sargassum, Turbinaria.
        
        Ishigeales Cho et al. 2004 [Ishigeacea Okamura 1935]. Ishige.
        
        Laminariales Migula 1908. Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
        
        Nemodermatales Parente et al. 2008. Nemoderma.
        
        Onslowiales Draisma & Prud'homme van Reine 2008. Onslowia.
        
        Ralfsiales Nakamura ex Lim & Kawai 2007. Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
        
        Scytothamnales Peters & Clayton 1998. Scytothamnus, Splachnidium, Stereocladon.
        
        Sphacelariales Migula 1908. Chaetopteris, Halopteris, Stypocaulon, Sphacelaria, Verosphacella.
        
        Sporochnales Sauvageau 1926. Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
        
        Syringodermatales Henry 1984. Syringoderma.
        
        Tilopteridales Bessey 1907. Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria, Tilopteris.
        
        Phaeosacciophyceae R.A.Andersen, L.Graf & H.S.Yoon 2020^[44]
        Phaeosaccionaceae J. Feldmann 1949. Phaeosaccion.
        
        Tetrasporopsidaceae R.A.Andersen, L.Graf & H.S.Yoon 2020. Tetrasporopsis, Psammochrysis, Chrysomeris.
        
        Phaeothamiophyceae Andersen & Bailey in Bailey et al. 1998
        Phaeothamniales Bourrelly 1954, emend. Andersen & Bailey in Bailey et al. 1998. Phaeothamnion.
        
        Pleurochloridales Ettl 1956. Pleurochloridella.
        
        Schizocladiophyceae Henry, Okuda & Kawai 2003. Schizocladia.
        
        Xanthophyceae Allorge 1930, emend. Fritsch 1935 [Heterokontae Luther 1899; Heteromonadea Leedale 1983; Xanthophyta Hibberd 1990]
        Tribonematales Pascher 1939. Botrydium, Bumilleriopsis, Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus, Tribonema, Xanthonema.
        
        Vaucheriales Bohlin 1901. Vaucheria.
  - Diatomista Derelle et al. 2016, emend. Cavalier-Smith 2017 [SIII clade]. Incertae sedis: environmental clades MOCH-1, MOCH-2 and MOCH-4 Massana et al. 2014.
    - Bolidophyceae Guillou et al. 1999 [Parmales Booth & Marchant 1987]. Bolidomonas, Triparma, Tetraparma, Pentalamina.
    - Diatomeae Dumortier 1821 [Bacillariophyta Haeckel 1878]
      - Leptocylindrophytina D.G. Mann, in Adl et al. 2019
        Leptocylindrophyceae D.G. Mann, in Adl et al. 2019. Leptocylindrus, Tenuicylindrus.
        
        Corethrophyceae D.G. Mann, in Adl et al. 2019. Corethron.
      - Ellerbeckiophytina D.G. Mann, in Adl et al. 2019. Ellerbeckia.
      - Probosciophytina D.G. Mann, in Adl et al. 2019. Proboscia.
      - Melosirophytina D.G. Mann, in Adl et al. 2019. Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia, Endictya.
      - Coscinodiscophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019. Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
      - Rhizosoleniophytina D.G. Mann, in Adl et al. 2019. Guinardia, Rhizosolenia, Pseudosolenia.
      - Arachnoidiscophytina D.G. Mann, in Adl et al. 2019. Arachnoidiscus.
      - Bacillariophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019
        Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
        Chaetocerotophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Chaetoceros, Bacteriastrum, Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë, Hydrosera.
        
        Lithodesmiophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Lithodesmium, Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
        
        Thalassiosirophycidae Round & R.M. Crawford in Round et al. 1990. Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella, Bacteriosira, Skeletonema, Detonula.
        
        Cymatosirophycidae Round & R.M. Crawford in Round et al. 1990. Cymatosira, Minutocellus, Papiliocellulus, Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella, Pierrecomperia.
        
        Odontellophycidae D. G. Mann, in Adl et al. 2019. Odontella, Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
        
        Chrysanthemodiscophycidae D.G. Mann, in Adl et al. 2019. Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus, Ardissonea, Climacosphenia, Toxarium.
        
        Biddulphiophyceae D. G. Mann, in Adl et al. 2019
        Biddulphiophycidae Round and R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Biddulphia.
        
        Attheya T. West 1860
        
        Bacillariophyceae Haeckel 1878, emend. Adl et al. 2019
        Striatellaceae Kützing 1844. Striatella, Pseudostriatella.
        
        Urneidophycidae Medlin 2016. (P?) Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis, Bleakeleya, Asterionellopsis.
        
        Fragilariophycidae Round in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia, Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira, Thalassionema.
        
        Bacillariophycidae D.G. Mann in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudonitzschia, Cylindrotheca, Navicula, Seminavis, Haslea, Stauroneis, Pleurosigma, Gyrosigma, Achnanthidium, Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella, Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella, etc.
    - Dictyochophyceae Silva 1980 [Silicoflagellata Lemmermann, 1901]
      - Dictyochales Haeckel 1894 [Dictyochida Borgert, 1891; Dictyochaceae Lemmermann, 1901]. Dictyocha.
      - Florenciellales Eikrem, Edvardsen & Throndsen 2007.^[45] Florenciella, Verrucophora.
      - Pedinellales Zimmermann et al. 1984 [Ciliophryida Febre-Chevalier, 1985; Actinomonadaceae Kent, 1880]. Actinomonas, Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella, Pteridomonas.
      - Rhizochromulinales O'Kelly & Wujek 1994 [Rhizochromulinaceae O'Kelly & Wujek, 1994]. Rhizochromulina.
    - Pelagophyceae Andersen & Saunders 1993
      - Pelagomonadales Andersen & Saunders 1993. Aureococcus, Pelagococcus, Pelagomonas.
      - Sarcinochrysidales Gayral & Billard 1977
        Sarcinochrysidaceae Gayral & Billard 1977. Ankylochrisis, Arachnochrysis, Aureoscheda, Aureoumbra, Nematochrysopsis, Pelagospilus, Pulvinaria, Sarcinochrysis, Sargassococcus.
        
        Chrysocystaceae M.Melkonian, H.S.Yoon & R.A.Andersen 2018.^[46] Chrysocystis, Chrysoreinhardia, Sungminbooa.

Alveolata Cavalier-Smith 1991

Colpodellida Cavalier-Smith 1993, emend. Adl et al. 2005, 2019
- Vitrellaceae Oborník & Lukeš 2012. Vitrella.
- Colpodellaceae Adl et al. 2019. Colpodella, Chilovora, Voromonas.
- Chromeraceae Oborník & Lukeš 2012. Chromera.
- Alphamonaceae Adl et al. 2019. Alphamonas.
Perkinsidae Levine 1978, emend. Adl et al. 2005 [Perkinsozoa Moestrup & Rehnstam-Holm 1999; Perkinsozoa Norén & Moestrup 1999]. Dinovorax, Parvilucifera, Perkinsus, ?Phagodinium, ?Psammosa, Rastrimonas, Snorkelia
Colponemida Cavalier-Smith 1993 emend. Adl et al. 2019 (P)
- Colponemidia Tikhonenkov et al. 2014. Colponema.
- Acavomonidia Tikhonenkov et al. 2014. Acavomonas.
- Palustrimonas Patterson & Simpson 1996
- Oxyrrhis Dujardin 1841 [Oxyrrhinaceae Sournia 1984]
Dinoflagellata Bütschli 1885, emend. Fensome et al. 1993, emend. Adl et al. 2005. Incertae sedis genera: free-living (Adenoides, Akashiwo, Amphidiniella, Ankistrodinium, Apicoporus, Archaeosphaerodiniopsis, Bispinodinium, Bysmatrum, Cabra, Cladopyxis, Crypthecodinium, Cucumeridinium, Dactylodinium, Dicroerisma, Gloeodinium, Grammatodinium, Gynogonadinium, Gyrodiniellum, Halostylodinium, Heterodinium, Moestrupia, Paragymnodinium, Phytodinium, Plagiodinium, Planodinium, Pileidinium, Pseudadenoides, Pseudothecadinium, Pyramidodinium, Rhinodinium, Roscoffia, Sabulodinium, Sphaerodinium, Spiniferodinium, Testudodinium, Thecadinium, Thecadiniopsis, Togula) and parasitic Blastodiniales Chatton 1906 [no longer valid] (Amyloodinium, Apodinium, Cachonella, Caryotoma, Crepidoodinium, Haplozoon, Oodinium, Myxodinium, Piscinoodinium, Protoodinium, Rhinodinium, Schyzochitriodinium, Stylodinium).
- Syndiniales Loeblich III 1976. Incertae sedis genera: Ichthyodinium and Ellobiopsidae (Ellobiopsis, Thalassomyces).
  - Euduboscquellidae Coats & Bachvaroff 2012. Euduboscquella, Dogelodinium, Keppenodinium.
  - Amoebophryidae Cachon 1964 [environmental Marine Alveolate Group II]. Amoebophrya.
  - Syndinidae Chatton 1910 [environmental Marine Alveolate Group IV]. Hematodinium, Syndinium, Solenodinium.
  - Sphaeriparaceae Loeblich III 1970. Atlanticellodinium, Sphaeripara.
- Noctilucales Haeckel 1894 [Noctiluciphyceae Fensome et al. 1993]. Abedinium, Cachonodinium, Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium, Pomatodinium, Scaphodinium, Spatulodinium.
- Dinophyceae Pascher 1914
  - Gymnodiniphycidae Fensome et al. 1993
    - Gymnodinium F. Stein 1878, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto. Barrufeta, Chytriodinium, Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium, Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Warnowia.
    - Amphidinium Claparède & Lachmann 1859, emend. Flø Jørgensen et al. 2004 sensu stricto
    - Gyrodinium Kofoid & Swezy 1921, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto
    - Kareniaceae Bergholtz et al. 2005. Brachidinium, Karenia, Karlodinium, Takayama.
    - Ceratoperidiniaceae Loeblich III 1980, emend. Reñé & de Salas 2013. Ceratoperidinium, Kirithra.
    - Torodiniales Boutrup, Moestrup & Daugbjerg 2016. Kapelodinium, Torodinium.
    - Levanderina Moestrup et al. 2014
    - Margalefidinium F. Gómez, Richlen & D.M. Anderson 2017
    - Cochlodinium F. Schütt emend. F. Gómez, Richlen & D.M. Anderson 2017 sensu stricto
    - Ptychodiscales Fensome et al. 1993. Achradina, Amphilothus, Balechina, Ptychodiscus, Sclerodinium.
    - Borghiellaceae Moestrup, Lindberg, & Daugbjerg 2009. Baldinia, Borghiella.
    - Tovelliaceae Moestrup et al. 2005. Bernardinium, Esoptrodinium, Jadwigia, Tovellia.
    - Suessiaceae Fensome et al. 1993, emend. Moestrup et al. 2009. Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis, Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
  - Peridiniphycidae Fensome et al. 1993
    - Gonyaulacales Taylor 1980. Alexandrium, Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma, Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium, Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
    - Peridiniales Haeckel 1894. Amphidiniopsis, Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea, Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium, Qia, Vulcanodinium.
    - Thoracosphaeraceae Schiller 1930. Aduncodinium, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium, Ensiculifera, Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria, Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
    - Podolampadaceae Lindemann 1928. Blepharocysta, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas.
    - Kryptoperidiniaceae Lindemann 1925 ["dinotoms"]. Blixaea, Durinskia, Galeidinium, Kryptoperidinium, Unruhdinium, etc.
    - Heterocapsaceae Fensome et al. 1993. Heterocapsa.
    - Amphidomataceae Sournia 1984. Amphidoma, Azadinium.
    - Oxytoxaceae Lindemann 1928. Corythodinium, Oxytoxum.
    - Centrodiniaceae Hernández-Becerril 2010. Centrodinium.
  - Dinophysales Kofoid 1926. Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia, Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma, Pseudophalacroma, Sinophysis, Triposolenia.
  - Prorocentrales Lemmermann 1910. Mesoporus, Prorocentrum.
Apicomplexa Levine 1980, emend. Adl et al. 2005. Incertae sedis genera: Aggregata^{[lower-alpha 15]} Frenzel 1885, Christalloidophora Dehorne 1934, Dobellia* Ikeda 1914, Echinococcidium* Porchet 1978, Globidiellum* Brumpt 1913, Joyeuxella* Brasil 1902, Rhabdospora* Laguesse 1906, Spermatobium* Eisen 1895, Spiriopsis* Arvy & Peters 1972, Spirogregarina* Wood & Herman 1943, Toxocystis* Léger & Duboscq 1910, Trophosphaera* Le Calvez 1939.
- ?Agamococcidiorida Levine 1979. Gemmocystis*, Rhytidocystis.
- ?Protococcidiorida Kheisin 1956. Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*, Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
- Aconoidasida Mehlhorn et al. 1980 [Hematozoa Vivier 1982] (P)
  - Haemospororida Danilewsky 1885. Dionisia*, Haemocystidium, Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus, Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
  - Piroplasmorida Wenyon 1926. Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*, Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
  - Nephromycida Cavalier-Smith 1993, emend. Adl et al. 2019. Nephromyces, Cardiosporidium.
- Conoidasida Levine 1988 (P)
  - Coccidia Leuckart 1879 (P)
    - Adeleorina Léger 1911. Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*, Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia, Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
    - Eimeriorina Léger 1911. Atoxoplasma, Barrouxia*, Besnoitia, Caryospora, Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*, Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora, Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella, Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*, Toxoplasma, Tyzzeria*, Wenyonella*.
  - Gregarinasina Dufour 1828 (P). Incertae sedis genera: Digyalum Koura et al. 1990, Exoschizon Hukui 1939.
    - Archigregarinorida Grassé 1953 (P). Filipodium, Meroselenidium, Merogregarina, Platyproteum, Selenidium, Selenocystis, Veloxidium.
    - Eugregarinorida Léger 1900 (P). Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola, Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina, Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora, Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis, Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina, Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina, Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia, Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus, Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora, Xiphocephalus, Zygosoma*, and more.
    - Neogregarinorida Grassé 1953. Apicystis, Aranciocystis, Caulleryella*, Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*, Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
    - Cryptogregarinorida Cavalier-Smith 2014, emend. Adl et al. 2019. Cryptosporidium.
  - Blastogregarinea Chatton and Villeneuve 1936, emend. Simdyanov et al. 2018. Chattonaria, Siedleckia.
Ciliophora Doflein 1901 [Ciliata Perty 1852; Infusoria Bütschli 1887]
- Postciliodesmatophora Gerassimova & Seravin 1976
  - Karyorelictea Corliss 1974
    - Kentrophoridae Jankowski 1980. Kentrophoros.
    - Loxodida Jankowski 1980
      - Cryptopharyngidae Jankowski 1980. Cryptopharynx.
      - Loxodidae Bütschli 1889. Loxodes.
    - Geleiidae Kahl 1933. Geleia.
  - Heterotrichea Stein 1859
    - Blepharismidae Jankowski in Small & Lynn 1985. Blepharisma
    - Climacostomidae Repak 1972. Climacostomum.
    - Condylostomatidae Kahl in Doflein & Reichenow 1929. Chattonidium, Condylostoma.
    - Fabreidae Shazib et al. 2014. Fabrea.
    - Gruberiidae Shazib et al. 2014. Gruberia.
    - Coliphorina Jankowski 1967
      - Folliculinidae Dons 1914. Folliculina.
      - Maristentoridae Miao et al. 2005. Maristentor.
    - Peritromidae Stein 1867. Peritromus.
    - Spirostomidae Stein 1867. Anigsteinia, Spirostomum.
    - Stentoridae Carus 1863. Stentor.
- Intramacronucleata Lynn 1996. Incertae sedis: Protocruziidae Jankowski 1980 [Protocruziidia de Puytorac et al. 1987] (Protocruzia Faria da Cunha & Pinto 1922).
  - SAL Gentekaki et al. 2014. Incertae sedis: Cariacotrichea Orsi et al. 2011 (Cariacothrix caudata), Mesodiniidae ankowski, 1980 (Mesodinium), Phacodiniidia Small and Lynn 1985 (Phacodinium).
    - Spirotrichea Bütschli 1889
      - Euplotia Jankowski 1979
        Euplotida Small & Lynn 1985
        Aspidiscidae Ehrenberg 1830. Aspidisca.
        
        Certesiidae Borror & Hill 1995. Certesia.
        
        Euplotidae Ehrenberg 1838. Euplotes.
        
        Gastrocirrhidae Fauré-Fremiet 1961. Gastrocirrhus.
        
        Uronychidae Jankowski 1975. Diophrys, Uronychia.
        
        Discocephalida
        Discocephalidae Jankowski 1979. Discocephalus, Prodiscocephalus, Paradiscocephalus.
        
        Pseudoamphisiellidae Song et al. 1997. Leptoamphisiella, Pseudoamphisiella.
      - Perilemmaphora Berger 2008
        Hypotrichia Stein 1859
        Stichotrichida Fauré-Fremiet 1961 (P)^{[lower-alpha 16]}
        Amphisiellidae Jankowski 1979. Amphisiella, Bistichella.
        
        Atractosidae Bourland 2015. Atractos.
        
        Epiclintidae Wicklow & Borror 1990. Epiclintes.
        
        Gonostomatidae Small & Lynn 1985. Cotterillia, Gonostomum.
        
        Halteriidae Claparède & Lachmann 1858. Halteria, Meseres.
        
        Holostichidae Fauré-Fremiet 1961. Holosticha, Uncinata.
        
        Kahliellidae Tuffrau 1979. Deviata, Kahliella.
        
        Keronidae Dujardin 1840. Kerona.
        
        Oxytrichidae Ehrenberg 1830 (P). Cyrtohymena, Gastrostyla, Oxytricha, Stylonychia.
        
        Parabirojimidae Dai & Xu 2011. Parabirojimia, Tunicothrix.
        
        Plagiotomidae Bütschli 1887. Plagiotoma.
        
        Psammomitridae Jankowski 1979. Psammomitra.
        
        Pseudoamphisiellidae Song et al. 1996. Pseudoamphisiella.
        
        Psilotrichidae Bütschli 1889. Psilotricha, Urospinula.
        
        Schmidingerotrichidae Foissner 2012. Schmidingerothrix.
        
        Spirofilidae von Gelei 1929. Spirofilopsis, Strongylidium.
        
        Trachelostylidae Small & Lynn 1985. Trachelostyla.
        
        Uroleptidae Foissner & Stoeck 2008. Paruroleptus, Uroleptus.
        
        Urostylida Jankowski 1979 (P)
        Bergeriellidae Liu et al. 2010. Bergeriella, Neourostylopsis.
        
        Hemicycliostylidae Lyu et al. 2018. Australothrix, Hemicycliostyla.
        
        Pseudokeronopsidae Borror & Wicklow, 1983. Apoholosticha, Pseudokeronopsis.
        
        Pseudourostylidae Jankowski 1979. Pseudourostyla.
        
        Urostylidae Bütschli 1889. Bakuella, Diaxonella, Urostyla.
        
        Oligotrichea Bütschli 1887
        Oligotrichida Bütschli 1887
        Cyrtostrombidiidae Agatha 2004. Cyrtostrombidium.
        
        Pelagostrombidiidae Agatha 2004. Pelagostrombidium.
        
        Strombidiidae Fauré-Fremiet 1970. Strombidium (P).
        
        Tontoniidae Agatha 2004. Laboea, Tontonia.
        
        Choreotrichida Small & Lynn 1985. Incertae sedis: Lynnella Liu et al. 2011 [Lynnellidae Liu et al. 2011; Lynnellida Liu et al. 2015]
        Strobilidiina Jankowski 1980 (P)
        Leegaardiellidae Lynn & Montagnes 1988. Leegaardiella.
        
        Lohmanniellidae Montagnes & Lynn 1991. Lohmanniella.
        
        Strobilidiidae Kahl in Doflein & Reichenow 1929. Strobilidium.
        
        Strombidinopsidae Small & Lynn 1985. Strombidinopsis (P).
        
        Tintinnina Kofoid & Campbell 1929. Incertae sedis: Helicostomella, Tintinnopsis (P), several other genera.
        Ascampbelliellidae Corliss 1960. Ascampbelliella
        
        Cyttarocylididae Kofoid & Campbell 1929 [probably synonymous with Petalotrichidae]. Cyttarocylis.
        
        Dictyocystidae Haeckel 1873. Dictyocysta.
        
        Epiplocylididae Kofoid & Campbell 1939. Epiplocylis.
        
        Eutintinnidae Bachy et al. 2012. Dartintinnus, Eutintinnus.
        
        Favellidae Kofoid & Campbell 1929. Favella.
        
        Nolaclusiliidae Sniezek et al. 1991. Nolaclusilis.
        
        Petalotrichidae Kofoid & Campbell 1929 [probably synonymous with Cyttarocylididae]. Petalotricha.
        
        Ptychocylididae Kofoid & Campbell 1929. Cymatocylis, Ptychocylis.
        
        Rhabdonellidae Kofoid & Campbell 1929. Metacylis, Rhabdonella, Schmidingerella.
        
        Stenosemellidae Campbell 1954 (P). Stenosemella.
        
        Tintinnidae Claparède & Lachmann 1858. Amphorellopsis, Salpingacantha, Salpingella, Tintinnus.
        
        Tintinnidiidae Kofoid & Campbell 1929. Tintinnidium.
        
        Undellidae Kofoid & Campbell 1929. Undella.
        
        Xystonellidae Kofoid & Campbell 1929. Dadayiella, Parafavella, Xystonella.
      - Licnophoridae Bütschli 1887. Licnophora, Prolicnophora.
      - Kiitrichidae Nozawa 1941. Caryotricha, Kiitricha.
    - Lamellicorticata Vd'ačný et al. 2010
      - Armophorea Lynn 2004. Incertae sedis: Mylestomatidae Kahl in Doflein & Reichenow, 1929 (Mylestoma).
        Metopida Jankowski 1980 (P)
        Metopidae Kahl 1927 (P). Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium, Tesnospira.
        
        Apometopidae Foissner 2016. Cirranter, Urostomides.
        
        Tropidoatractidae Rotterová et al. 2018. Palmarella, Tropidoatractus.
        
        Clevelandellida de Puytorac & Grain 1976
        Clevelandellidae Kidder 1938. Clevelandella.
        
        Inferostomatidae Ky 1971. Inferostoma.
        
        Neonyctotheridae Affa'a 1987. Neonyctotherus.
        
        Nyctotheridae Amaro 1972 (P). Nyctotherus.
        
        Sicuophoridae Amaro 1972. Sicuophora.
        
        Caenomorphidae Poche 1913. Caenomorpha, Ludio, Sulfonecta.
        
        Odontostomatida Sawaya 1940
        Discomorphellidae Corliss 1960. Discomorphella.
        
        Epalxellidae Corliss 1960. Epalxella, Saprodinium.
      - Litostomatea Small & Lynn 1981
        Rhynchostomatia Jankowski 1980
        Dileptida Jankowski 1978
        Dileptidae Jankowski 1980. Apodileptus, Dileptus, Pseudomonilicaryon.
        
        Dimacrocaryonidae Jankowski 1978. Dimacrocaryon, Monomacrocaryon, Rimaleptus.
        
        Tracheliidae Ehrenberg 1838. Trachelius.
        
        Haptoria Corliss 1974 (P). Incertae sedis: Chaenea.
        Lacrymariidae de Fromentel 1876. Lacrymaria.
        
        Haptorida Corliss 1974
        Enchelyodonidae Foissner et al. 2002. Enchelyodon, Fuscheria.
        
        Homalozoonidae Jankowski 1980. Homalozoon.
        
        Pleuroplitidae Foissner 1996. Pleuroplites.
        
        Didiniidae Poche 1913. Didinium, Monodinium.
        
        Pleurostomatida Schewiakoff 1896
        Amphileptidae Bütschli 1889. Amphileptus.
        
        Litonotidae Kent 1882. Litonotus.
        
        Kentrophyllidae Wu et al. 2015. Epiphyllum, Kentrophyllum.
        
        Spathidiida Foissner & Foissner 1988
        Acropisthiidae Foissner & Foissner 1988. Acropisthium, Chaenea.
        
        Actinobolinidae Kahl 1930. Actinobolina.
        
        Apertospathulidae Foissner et al. 2005. Apertospathula.
        
        Enchelyidae Ehrenberg 1838. Enchelys.
        
        Pseudoholophryidae Berger et al. 1984. Pseudoholophrya.
        
        Spathidiidae Kahl in Doflein & Reichenow 1929. Legendrea,^[47] Spathidium.
        
        Trachelophyllidae Kent 1882. Trachelophyllum.
        
        Helicoprorodontidae Small & Lynn 1985
        
        Trichostomatia Bütschli 1889
        Vestibuliferida de Puytorac et al. 1974
        Balantidiidae Reichenow in Doflein and Reichenow 1929. Balantidium, Neobalantidium (P).
        
        Buetschliidae Poche 1913. Buetschlia.
        
        Paraisotrichidae da Cunha 1917. Paraisotrichia.
        
        Protocaviellidae Grain in Corliss 1979. Protocaviella.
        
        Protohalliidae da Cunha & Muniz 1927. Protohallia.
        
        Pycnotrichidae Poche 1913. Pycnothrix, perhaps Buxtonella.
        
        Isoendo
        Isotrichidae Bütschli 1889. Dasytricha, Isotricha.
        
        Entodiniomorphida Reichenow in Doflein & Reichenow 1929
        Blepharocorythina Wolska 1971
        Blepharocorythidae Hsiung 1929. Blepharocorys.
        
        Parentodiniidae Ito, Miyazaki & Imai 2002. Parentodinium.
        
        Pseudoentodiniidae Wolska 1986. Pseudoentodinium.
        
        Entodiniomorphina Reichenow in Doflein & Reichenow 1929
        Cycloposthiidae Poche 1913. Cycloposthium.
        
        Gilchristidae Ito, Ishihara & Imai 2014. Gilchristia.
        
        Ophryoscolecidae Stein 1859. Entodinium, Ophryoscolex, Polyplastron.
        
        Polydiniellidae Corliss 1960. Polydiniella.
        
        Rhinozetidae Van Hoven, Gilchrist & Hamilton-Attwell 1988. Rhinozeta.
        
        Spirodiniidae Strelkow 1939. Spirodinium.
        
        Telamodiniidae Latteur & Dufey 1967. Telamodinium.
        
        Troglodytellidae Corliss 1979. Troglodytella,.
        
        Macropodiniida Lynn 2008
        Amylovoracidae Cameron & O'Donoghue 2002. Amylovorax.
        
        Macropodiniidae Dehority 1996. Macropodinium.
        
        Polycostidae Cameron & O'Donoghue 2003. Polycosta.
  - CONTHREEP Lynn in Adl et al. 2012 [Ventrata Cavalier-Smith 2004]. Incertae sedis: Askenasia Blochmann 1895, Cyclotrichiidae Jankowski 1980 (Cyclotrichium), Paraspathidium Noland 1937, Pseudotrachelocercidae Song 1990 (Pseudotrachelocerca), Discotrichidae Jankowski 1967 [Discotrichida Fan et al. 2014] (Discotricha, Lopezoterenia).
    - Phyllopharyngea de Puytorac et al. 1974
      - Synhymeniida de Puytorac et al. in Deroux 1978
        Nassulopsidae Deroux in Corliss 1979. Nassulopsis.
        
        Orthodonellidae Jankowski 1968. Orthodonella, Zosterodasys.
        
        Scaphidiodontidae Deroux in Corliss 1979. Chilodontopsis, Scaphidiodon.
        
        Synhymeniidae Jankowski in Small & Lynn 1985. Synhymenia.
      - Subkinetalia Gong et al. 2009
        Cyrtophoria Fauré-Fremiet in Corliss 1956
        Chlamydodontida Deroux 1976 (P)
        Chilodonellidae Deroux 1970. Chilodonella.
        
        Chitonellidae Small & Lynn 1985. Chitonella.
        
        Chlamydodontidae Stein 1859. Chlamydodon.
        
        Gastronautidae Deroux 1994. Gastronauta.
        
        Kryoprorodontidae Alekperov & Mamajeva 1992. Gymnozoum.
        
        Lynchellidae Jankowski 1968. Chlamydonella, Lynchella.
        
        Dysteriida Deroux 1976
        Dysteriidae Claparède & Lachmann 1858. Dysteria (P), Trochilia.
        
        Hartmannulidae Poche 1913 (P). Hartmannula.
        
        Kyaroikeidae Sniezek & Coats 1996. Kyaroikeus.
        
        Plesiotrichopidae Deroux 1976. Plesiotrichopus.
        
        Chonotrichia Wallengren 1895
        Exogemmida Jankowski 1972
        Chilodochonidae Wallengren 1895. Chilodochona.
        
        Filichonidae Jankowski 1973. Filichona.
        
        Helichonidae Jankowski 1972. Heliochona.
        
        Lobochonidae Jankowski 1967. Lobochona.
        
        Phyllochonidae Jankowski 1972. Phyllochona.
        
        Spirochonidae Stein 1854. Spirochona.
        
        Cryptogemmida Jankowski 1975
        Actinichonidae Jankowski 1973. Actinichona.
        
        Echinichonidae Jankowski 1973. Echinichona.
        
        Inversochonidae Jankowski 1973. Inversochona.
        
        Isochonidae Jankowski 1973. Isochona.
        
        Isochonopsidae Batisse & Crumeyrolle 1988. Isochonopsis.
        
        Stylochonidae Mohr 1948. Stylochona.
        
        Rhynchodia Chatton & Lwoff 1939
        Hypocomidae Bütschli 1889. Hypocoma.
        
        Rhynchodida Chatton & Lwoff 1939
        Ancistrocomidae Chatton & Lwoff 1939. Ancistrocoma.
        
        Sphenophryidae Chatton & Lwoff 1921. Sphenophrya.
        
        Suctoria Claparède & Lachmann 1858
        Exogenida Collin 1912
        Allantosomatidae Jankowski 1967. Allantosoma.
        
        Dentacinetidae Batisse 1992. Dentacineta.
        
        Dendrosomididae Jankowski 1978. Dendrosomides.
        
        Ephelotidae Kent 1882. Ephelota.
        
        Lecanophryidae Jankowski 1973. Lecanophrya.
        
        Manuelophryidae Dovgal 2002. Manuelophrya.
        
        Metacinetidae Bütschli 1889. Metacineta.
        
        Ophryodendridae Stein 1867. Ophryodendron.
        
        Paracinetidae Jankowski 1978. Paracineta.
        
        Phalacrocleptidae Kozloff 1966. Phalacrocleptes.
        
        Podophryidae Haeckel 1866. Podophrya.
        
        Praethecacinetidae Dovgal 1996. Praethecacineta.
        
        Rhabdophryidae Jankowski 1970. Rhabdophrya.
        
        Severonidae Jankowski 1981. Severonis.
        
        Spelaeophryidae Jankowski in Batisse 1975. Spelaeophrya.
        
        Tachyblastonidae Grell 1950. Tachyblaston.
        
        Thecacinetidae Matthes 1956. Thecacineta.
        
        Endogenida Collin 1912
        Acinetidae Stein 1859. Acineta.
        
        Acinetopsidae Jankowski 1978. Acinetopsis.
        
        Choanophryidae Dovgal 2002. Choanophrya.
        
        Corynophryidae Jankowski 1981. Corynophrya.
        
        Dactylostomatidae Jankowski 1978. Dactylostoma.
        
        Dendrosomatidae Fraipont 1878. Dendrosoma.
        
        Endosphaeridae Jankowski in Corliss 1979. Endosphaera.
        
        Erastophryidae Jankowski 1978. Erastophrya.
        
        Pseudogemmidae Jankowski 1978. Pseudogemma.
        
        Rhynchetidae Jankowski 1978. Rhyncheta.
        
        Solenophryidae Jankowski 1981. Solenophrya.
        
        Tokophryidae Jankowski in Small & Lynn 1985. Tokophrya.
        
        Trichophryidae Fraipont 1878. Trichophrya.
        
        Evaginogenida Jankowski in Corliss 1979
        Cometodendridae Jankowski 1978. Cometodendron.
        
        Cyathodiniidae da Cuhna 1914. Cyathodinium.
        
        Dendrocometidae Haeckel 1866. Dendrocometes.
        
        Discophryidae Collin 1912. Discophrya.
        
        Enchelyomorphidae Augustin & Foissner 1992. Enchelyomorpha.
        
        Heliophryidae Corliss 1979. Heliophrya.
        
        Periacinetidae Jankowski 1978. Periacineta.
        
        Prodiscophryidae Jankowski 1978. Prodiscophrya.
        
        Rhynchophryidae Jankowski 1978. Rhynchophrya.
        
        Stylocometidae Jankowski 1978. Stylocometes.
        
        Trypanococcidae Dovgal 2002. Trypanococcus.
    - Colpodea Small & Lynn 1981
      - Bursariomorphida Fernández-Galiano 1978
        Bryometopidae Jankowski 1980. Bryometopus (P), Thylakidium.
        
        Bursaridiidae Foissner 1993. Bursaridium, Paracondylostoma.
        
        Bursariidae Bory de St. Vincent 1826. Bursaria.
      - Colpodida de Puytorac et al. 1974. Incertae sedis: Bardeliellidae Foissner 1984 (Bardeliella), Hausmanniellidae Foissner 1987 (Avestina, Hausmanniella), Ilsiellidae Bourland et al. 2011 (Ilsiella), Pseudochlamydonellidae Buitkamp et al. 1989 (Hackenbergia, Pseudochlamydonella) and Marynidae Poche 1913 (Maryna).
        Bryophryina de Puytorac et al. 1979
        Bryophryidae de Puytorac et al. 1979. Bryophrya.
        
        Sandmanniellidae Foissner & Stoeck 2009. Sandmanniella.
        
        Colpodina Foissner et al. 2011
        Colpodidae Bory de St. Vincent 1826 (P). Colpoda.
        
        Grandoriidae Corliss 1960. Grandoria.
        
        Tillinidae Foissner et al. 2011. Tillina.
        
        Grossglockneriidae Foissner 1980 [Grossglockneriina Foissner 1980]. Grossglockneria, Pseudoplatyophrya.
      - Cyrtolophosidida Foissner 1978
        Cyrtolophosididae Stokes 1888. Cyrtolophosis.
        
        Kreyellidae Foissner 1979. Kreyella.
      - Platyophryida de Puytorac et al. 1979
        Ottowphryidae Foissner et al. 2011. Ottowphrya, Platyophryides.
        
        Platyophryidae de Puytorac et al. 1979 (P). Platyophrya.
        
        Sagittariidae Grandori & Grandori 1935. Sagittaria.
        
        Sorogenidae Bradbury & Olive 1980. Sorogena.
        
        Woodruffiidae Gelei 1954. Etoschophrya, Rostrophrya, Woodruffia.
    - Nassophorea (P)
      - Colpodidiidae Foissner 1995. Colpodidium.
      - Nassulida Jankowski 1967
        Furgasoniidae Corliss 1979. Furgasonia, Wolfkosia.
        
        Nassulidae de Fromentel 1874. Nassula, Obertrumia.
      - Microthoracida Jankowski 1967
        Microthoracidae Wrzesniowski 1870. Drepanomonas, Microthorax.
        
        Leptopharyngidae Kahl 1926. Leptopharynx, Pseudomicrothorax.
    - Prostomatea Schewiakoff 1896 (P)
      - Apsiktratidae Foissner et al. 1994 [Prostomatida Schewiakoff 1896]
        Balanionidae Small & Lynn 1985. Balanion.
        
        Cryptocaryonidae Wright & Colorni 2002. Cryptocaryon.
        
        Colepidae Ehrenberg 1838. Coleps, Plagiopogon.
        
        Holophryidae Perty 1852. Holophrya.
        
        Lagynidae Sola et al. 1990. Lagynus.
        
        Metacystidae Kahl 1926. Metacystis, Vasicola.
        
        Placidae Small & Lynn 1985. Placus.
        
        Plagiocampidae Kahl 1926. Plagiocampa.
        
        Prorodontidae Kent 1881. Prorodon.
        
        Urotrichidae Small & Lynn 1985. Urotricha.
    - Plagiopylea Small & Lynn 1985
      - Plagiopylida Small & Lynn 1985
        Epalxellidae Corliss 1960. Epalxella, Saprodinium.
        
        Plagiopylidae Schewiakoff 1896. Plagiopyla.
        
        Sonderiidae Small & Lynn 1985. Sonderia.
        
        Trimyemidae Kahl 1933. Trimyema.
    - Oligohymenophorea de Puytorac et al. 1974
      - Apostomatia Chatton & Lwoff 1928
        Apostomatida Chatton & Lwoff 1928
        Colliniidae Cépède 1910. Collinia, Metacollinia.
        
        Cyrtocaryidae Corliss 1979. Cyrtocaryum.
        
        Foettingeriidae Chatton 1911. Foettingeria.
        
        Pseudocolliniidae Chantangsi et al. 2013. Fusiforma, Pseudocollinia.
        
        Astomatophorida Jankowski 1966
        Opalinopsidae Hartog 1906. Opalinopsis.
        
        Pilisuctorida Jankowski 1966
        Conidophryidae Kirby 1941. Conidophrys.
      - Astomatia Schewiakoff 1896
        Anoplophryidae Cépède 1910. Anoplophrya.
        
        Buetschliellidae de Puytorac in Corliss 1979. Buetschliella.
        
        Clausilocolidae de Puytorac in Corliss 1979. Clausilocola.
        
        Contophryidae de Puytorac 1972. Contophyra.
        
        Haptophryidae Cépède 1923. Haptophrya.
        
        Hoplitophryidae Cheissin 1930. Hoplitophrya.
        
        Intoshellinidae Cépède 1910. Intoshellina.
        
        Maupasellidae Cépède 1910. Maupasella.
        
        Radiophryidae de Puytorac 1972. Radiophrya.
      - Hymenostomatia Delage & Hérouard 1896
        Tetrahymenida Fauré-Fremiet in Corliss 1956. Incertae sedis: Trichospiridae Kahl 1926 (Trichospira).
        Curimostomatidae Jankowski 1968. Curimostoma.
        
        Glaucomidae Corliss 1971. Glaucoma.
        
        Spirozonidae Kahl 1926. Spirozona.
        
        Tetrahymenidae Corliss 1952. Tetrahymena.
        
        Turaniellidae Didier 1971. Colpidium, Dexiostoma, Turaniella.
        
        Ophryoglenida Canella 1964
        Ichthyophthiriidae Kent 1881. Ichthyophthirius.
        
        Ophryoglenidae Kent 1881. Ophryoglena.
      - Peniculia Fauré-Fremiet in Corliss 1956 (P)
        Peniculida Fauré-Fremiet in Corliss 1956
        Clathrostomatidae Kahl 1926. Clathrostoma.
        
        Frontoniidae Kahl 1926. Disematostoma, Frontonia (P).
        
        Lembadionidae Jankowski in Corliss 1979. Lembadion.
        
        Maritujidae Jankowski in Small & Lynn 1985. Marituja.
        
        Neobursaridiidae Dragesco & Tuffrau 1967. Neobursaridium.
        
        Parameciidae Dujardin 1840. Paramecium.
        
        Paranassulidae Fauré-Fremiet 1962. Paranassula.
        
        Stokesiidae Roque 1961. Stokesia.
        
        Urocentridae Claparède & Lachmann 1858 [Urocentrida de Puytorac, Grain & Mignot 1987]
      - Peritrichia Stein 1859
        Sessilida Kahl 1933
        Astylozoidae Kahl 1935. Astylozoon, Hastatella.
        
        Ellobiophryidae Chatton and Lwoff 1929. Ellobiophrya.
        
        Epistylididae Kahl 1933. Epistylis.
        
        Lagenophryidae Bütschli 1889. Lagenophrys.
        
        Operculariidae Fauré-Fremiet in Corliss 1979. Opercularia.
        
        Rovinjellidae Matthes 1972. Rovinjella.
        
        Scyphidiidae Kahl 1933 (P). Scyphidia.
        
        Termitophryidae Lom in Corliss 1979. Termitophrya.
        
        Usconophryidae Clamp 1991. Usconophrys.
        
        Vaginicolidae de Fromentel 1874. Cothurnia, Pyxicola, Thuricola, Vaginicola.
        
        Vorticellidae Ehrenberg 1838. Carchesium, Epicarchesium (P), Ophrydium, Pelagovorticella, Pseudovorticella (P), Vorticella (P).
        
        Zoothamniidae Sommer 1951. Haplocaulus, Zoothamnium.
        
        Mobilida Kahl 1933
        Polycyclidae Poljansky 1951. Polycycla.
        
        Trichodinidae Claus 1874. Trichodina.
        
        Trichodinopsidae Kent 1881. Trichodinopsis.
        
        Urceolariidae Dujardin 1840. Leiotrocha, Urceolaria.
      - Scuticociliatia Small 1967 (P)
        Philasterida Small 1967
        Cohnilembidae Kahl 1933. Cohnilembus.
        
        Cryptochilidae Berger in Corliss 1979. Cryptochilum.
        
        Entodiscidae Jankowski 1973. Entodiscus.
        
        Entorhipidiidae Madsen 1931. Entorhipidium.
        
        Orchitophryidae Cépède 1910 (P). Orchitophrya.
        
        Paralembidae Corliss & de Puytorac in Small & Lynn 1985. Anophrys, Paralembus.
        
        Parauronematidae Small & Lynn 1985 (P). Parauronema (P).
        
        Philasteridae Kahl 1931. Kahlilembus, Philaster.
        
        Pseudocohnilembidae Evans & Thompson 1964. Pseudocohnilembus.
        
        Schizocaryidae Jankowski 1979. Schizocaryum.
        
        Thigmophryidae Chatton & Lwoff 1926. Thigmophrya.
        
        Thyrophylacidae Berger in Corliss 1961. Thyrophylax.
        
        Uronematidae Thompson 1964. Uronema.
        
        Urozonidae Grolière 1975. Urozona.
        
        Pleuronematida Fauré-Fremiet in Corliss 1956
        Calyptotrichidae Small & Lynn 1985. Calyptotricha.
        
        Conchophthiridae Kahl in Doflein and Reichenow 1929. Conchophthirus.
        
        Ctedoctematidae Small & Lynn 1985. Ctedoctema.
        
        Cyclidiidae Ehrenberg 1838 (P). Cristigera, Cyclidium.
        
        Dragescoidae Jankowski 1980. Dragescoa.
        
        Eurystomatellidae Miao et al. 2010. Eurystomatella.
        
        Histiobalantiidae de Puytorac & Corliss in Corliss 1979. Histiobalantium.
        
        Peniculistomatidae Fenchel 1965. Peniculistoma.
        
        Pleuronematidae Kent 1881 (P). Pleuronema.
        
        Thigmocomidae Kazubski 1958. Thigmocoma.
        
        Thigmotrichida Chatton & Lwoff 1922
        Ancistridae Issel 1903. Ancistrum.
        
        Hemispeiridae König 1894. Hemispeira.
        
        Hysterocinetidae Diesing 1866. Hysterocineta.
        
        Paraptychostomidae Ngassam et al. 1994. Paraptychostomum.
        
        Loxocephalida Jankowski 1964 (P)
        Cinetochilidae Perty 1852 (P). Cinetochilum, Sathrophilus.
        
        Loxocephalidae Jankowski 1964. Cardiostomatella, Dexiotricha, Loxocephalus.

Rhizaria Cavalier-Smith 2002

?Gymnosphaerida Poche 1913, emend. Mikrjukov 2000. Actinocoryne, Cienkowskya, Gymnosphaera, Hedraiophrys [possible synonym of Cienkowskya], Wagnerella.
Cercozoa^{[lower-alpha 17]} Cavalier-Smith 1998, emend. Adl et al. 2005; emend. Cavalier-Smith 2018^[48] [Filosa Cavalier-Smith & Chao 2003]. Incertae sedis cercozoan genera: ?Dictiomyxa, ?Katabia, ?Myxodictyium, ?Pontomyxa, ?Protomyxa, ?Protogenes, ?Pseudospora, ?Rhizoplasma.
- ?Discocelia Cavalier-Smith 2013 [Discocelis Vørs 1988]
- ?Psammonobiotidae* Golemansky 1974, emend. Meisterfeld 2002. Alepiella, Chardezia, Edaphonobiotus, Feuerbornia, Frenzelina, Lesquerella, Micramphora, Micropsammella, Nadinella, Ogdeniella, Psammonobiotus, Propsammonobiotus, Rhumbleriella.
- Sarcomonadea Cavalier-Smith 1993 emend. Cavalier-Smith 2018 (P)
  - Cercomonadida^{[lower-alpha 7]} Poche 1913, emend. Vickerman 1983, emend. Mylnikov 1986, emend. Karpov et al. 2006; emend Howe et al. 2009; emend Cavalier-Smith 2012 [Cercomonadidae Kent 1880, emend. Mylnikov and Karpov 2004; Cercobodonidae Hollande 1942]. Cercomonas, Eoercomonas, Filomonas, Neocercomonas, Cavernomonas.
  - Paracercomonadida Cavalier-Smith 2018 [Paracercomonadidae Cavalier-Smith & Karpov 2012]. Brevimastigomonas, Metabolomonas, Nucleocercomonas, Paracercomonas, Phytocercomonas.
  - Glissomonadida Howe & Cavalier-Smith 2009 [Heteromitidae Kent 1880, emend. Mylnikov 1990, emend. Mylnikov & Karpov 2004]
    - Saccharomycomorphidae Feng, He, Jiang, Zhang & Yu 2021.^[50] Saccharomycomorpha.
    - Sandonidae Howe et al. 2009. Sandona, Flectomonas, Neoheteromita, Mollimonas.
    - Dujardinidae Howe & Cavalier-Smith 2011. Dujardina.
    - Bodomorphidae Hollande 1952, emend. Cavalier-Smith in Howe et al. 2009. Bodomorpha.
    - Proleptomonadidae Howe et al. 2009. Proleptomonas.
    - Allapsidae Howe & Cavalier-Smith 2009. Allapsa, Teretomonas, Allantion.
  - Viridiraptoridae Hess & Melkonian 2013. Orciraptor, Viridiraptor.
  - Pansomonadidae Vickerman in Vickerman et al. 2005. Agitata, Aurigamonas.
- Sainouroidea Schuler et al. 2018 [Helkesida Cavalier-Smith 2018]
  - Sainouridae Cavalier-Smith 2008. Acantholus, Cholamonas, Homocognata, Sainouron.
  - Helkesimastigidae Cavalier-Smith 2008. Helkesimastix.
  - Guttulinopsidae Olive 1970. Guttulinopsis, Olivorum, Puppisaman, Rosculus.
- Thecofilosea Cavalier-Smith 2003, emend. Cavalier-Smith 2011
  - ?Mataza
  - Phaeodarea Haeckel 1879 [Tripylea Hertwig 1879]
    - Phaeoconchia Haeckel 1879. Coelodendrum, Coelographis, Conchellium, Conchopsis.
    - Phaeocystina Haeckel 1879. Aulacantha, Aulographis, Cannoraphis.
    - Phaeogromia Haeckel 1879. Castanella, Challengeron, Haeckeliana, Medusetta, Tuscarora.
    - Phaeosphaeria Haeckel 1879. Aulosphaera, Cannosphaera, Sagosphaera.
  - Cryomonadida Cavalier-Smith 1993
    - Rhogostomidae Dumack et al. 2017. Rhogostoma, Sacciforma, Capsellina.
    - Protaspidae Cavalier-Smith 1993 [Cryomonadidae Cavalier-Smith 1993]. Cryothecomonas, Protaspa.
  - Ventricleftida Cavalier-Smith 2011
    - Ventrifissuridae Cavalier-Smith 2018. Ventrifissura.
    - Verrucomonadidae Cavalier-Smith 2018. Verrucomonas.
  - Tectofilosida Cavalier-Smith 2003
    - Chlamydophryidae De Saedeleer, 1934. Chlamydophryse, Diaphoropodon, Lecythium, Trachyrhizium.
    - Psammonobiotidae Golemansky, 1974. Micropsamella.
    - ?Volutellidae Sudzuki, 1979. Pseudovolutella, Volutella.
    - Fiscullina Cavalier-Smith 2018
      - Fiscullidae Dumack, Mausbach and Bonkowski in Dumack et al. 2017. Fisculla, Omnivora.^[51]
      - Pseudodifflugiidae De Saedeleer 1934. Pseudodifflugia.
      - Rhizaspididae Skuja 1948. Rhizaspis.
  - Ebriacea Lemmermann 1901 [Ebriidae Poche 1913; Ebriida Deflandre 1936]. Ebria, Hermesinum, Botuliforma.
- Imbricatea Cavalier-Smith 2011
  - Spongomonadida Hibberd 1983 [Spongomonadidae Karpov 1990]. Rhipidodendron, Spongomonas.
  - Marimonadida Cavalier-Smith & Bass 2011
    - Abolliferidae Cavalier-Smith 2018. Abollifer, Cowlomonas, ?Heterochromonas.
    - Auranticordidae Cavalier-Smith 2018. Auranticordis, Rhabdamoeba.
    - Cyranomonadidae Cavalier-Smith 2018. Cyranomonas.
    - Pseudopirsoniidae Cavalier-Smith 2018. Pseudopirsonia.
  - Variglissida Cavalier-Smith 2014
    - Clautriaviidae Cavalier-Smith in Cavalier-Smith and Scoble, 2013. Clautriavia.
    - Nudifilidae Cavalier-Smith in Howe et al., 2011. Nudifila.
    - Quadriciliidae Cavalier-Smith 2018. Quadricilia.
  - Silicofilosea Adl et al. 2005, emend. Adl et al. 2012
    - Thaumatomonadida Shirkina 1987 [Thaumatomastigidae Patterson and Zoelfell 1991]
      - Thaumatomonadidae Hollande 1952. Allas, Hyaloselene, Reckertia, Thaumatomonas, Thaumatomastix, Ovaloplaca, Scutellomonas, Thaumatospina, Penardeugenia.
      - Peregriniidae Cavalier-Smith 2011. Gyromitus, Peregrinia.
      - Esquamulidae Shiratori, Yabuki & Ishida 2012. Esquamula.
    - Euglyphida Copeland 1956, emend. Cavalier-Smith 1997. Incertae sedis: Phaeobola.^[52]
      - Cyphoderiidae de Saedeleer 1934. Campascus*, Corythionella, Cyphoderia, Messemvriella*, Pseudocorythion, Schaudinnula*.
      - Paulinellidae de Saedeleer 1934, emend. Adl et al. 2012. Micropyxidiella, Ovulinata, Paulinella.
      - Euglyphina Kosakyan et al. 2016
        Assulinidae Lara et al. 2007. Assulina, Placocista, Valkanovia*.
        
        Sphenoderiidae Chatelain et al. 2013. Sphenoderia, Trachelocorythion, Deharvengia*.
        
        Trinematidae Hoogenraad & De Groot 1940, emend Adl et al. 2012. Corythion, Playfairina*, Puytoracia*, Trinema.
        
        Euglyphidae Wallich 1864, emend Lara et al. 2007. Euglypha, Scutiglypha.
        
        Tracheleuglypha^{[lower-alpha 18]} Deflandre 1928
    - Trivalvulariida Siemensma & Dumack 2020.^[53] Leptogromia, Trivalvularis.
- Metromonadea Cavalier-Smith 2007, emend. Cavalier-Smith 2011. Metromonas, Metopion, Micrometopion, Kiitoksia.
- Granofilosea Cavalier-Smith & Bass 2009.^[54] Incertae sedis granofilosean genera*: ?Apogromia, ?Kibisidytes, ?Leucodictyon, ?Limnofila, ?Mesofila, ?Microcometes, ?Microgromia, ?Nanofila, ?Reticulamoeba and probably ?Belaria, ?Ditrema, ?Heliomorpha [=Dimorpha] and ?Paralieberkuehnia.
  - Massisteridae Cavalier-Smith 1993. Massisteria, Minimassisteria.
  - Clathrulinidae Claus 1874 [Desmothoracida Hertwig and Lesser 1874]. Actinosphaeridium, Cienkowskya*, Clathrulina, Hedriocystis, Penardiophrys, ?Servetia.
- Chlorarachnea Hibberd & Norris 1984. Amorphochlora, Bigelowiella, Chlorarachnion, Cryptochlora, Gymnochlora, Lotharella, Minorisa, Partenskyella, Viridiuvalis.
Endomyxa^{[lower-alpha 17]} Cavalier-Smith 2002, emend. Bass & Berney in Adl et al. 2019.
- Vampyrellida West 1901, emend. Hess et al. 2012 [Aconchulinida De Saedeleer 1934]. Incertae sedis: Arachnula, Gobiella, Lateromyxa, Penardia.^[55]
  - Thalassomyxa Grell 1985
  - Vampyrellidae Zopf 1885. Vampyrella.
  - Leptophryidae Hess, Sausen & Melkonian 2012. Arachnomyxa, Leptophrys, Planctomyxa, Platyreta, Pseudovampyrella,^[56] Theratromyxa, Vernalophrys.
  - Placopodidae Jahn 1928 [Hyalodiscidae Poche 1913]. Placopus.
  - Sericomyxidae More, Simpson & Hess 2021. Sericomyxa.
- Phytomyxea Engler & Prantl 1897
  - Marinomyxa Kolátková, Čepička, Hoffman & Vohník 2021^[57]
  - Plasmodiophorida Cook 1928 [Plasmodiophorales Engl. 1892;^[58] Plasmodiophoromycota R.H. Whittaker 1969^[1]]. Plasmodiophora [Ostenfeldiella], Polymyxa, Woronina, Ligniera [Anisomyxa; Rhizomyxa; Sorolpidium], Sorosphaerula [Tuburcinia; Sorosporium], Spongospora [Clathrosorus], ?Membranosorus, ?Octomyxa, ?Polymyxa, ?Sorodiscus, ?Tetramyxa [Molliardia; Thecaphora].^[59]^[60]^[61]
  - Phagomyxida Cavalier-Smith 1993. Phagomyxa, Maullinia.
- Filoreta Bass & Cavalier-Smith 2009
- Gromia Dujardin 1835
- Ascetosporea Sprague 1979, emend. Cavalier-Smith 2009
  - Haplosporida Caullery & Mesnil 1899. Bonamia, Haplosporidium, Minchinia, Urosporidium.
  - Mikrocytida Hartikainen et al. 2013. Mikrocytos, Paramikrocytos.
  - Paramyxida Chatton 1911. Marteilia, Paramyxa, Paramarteilia, Marteilioides, Eomarteilia.
  - Claustrosporidium Larsson 1987
  - Paradiniida Schiller 1935. Paradinium.
Retaria Cavalier-Smith 2002
- Foraminifera d'Orbigny 1826. Incertae sedis groups: ?Lagenida, ?Heterogromia, ?Komokiacea*.
  - Monothalamids Pawlowski et al. 2013 (P) [currently under revision].^[62] All genera traditionally in Allogromiida, Astrorhizida, and the Xenophyophorea. Genera unplaced into families: Allogromia, Astrammina, Crithionina, Notodendrodes, Psammophaga, Bathysiphon.
    - Nujappikia Gooday & Holzmann 2022^[63]
    - Allogromiidae Rhumbler 1904. Vellaria.^[64]
    - Lieberkuehniidae Siemensma et al. 2021.^[65] Lieberkuehnia, Claparedellus.
    - Edaphoallogromiidae Siemensma et al. 2021.^[65] Edaphoallogromia.
    - Lacogromiidae Siemensma & Holzmann 2021.^[65] Lacogromia.
    - Limnogromiidae Holzmann & Siemensma 2021.^[65] Limnogromia.
    - Reticulomyxidae Page 1987, emend. Hülsmann 2014. Reticulomyxa, Dracomyxa, Haplomyxa,^[66] Wobo.
    - Schizamminidae Nørvang, 1961. Jullienella, Schizammina, Spiculosiphon.^[67]
    - Velamentofexidae Völcker & Clauß 2021.^[65] Velamentofex.
  - Tubothalamea Pawlowski et al. 2012. †Fusulinida Delage & Hérouard 1896 probably belongs to this group.^[3]
    - Miliolida Delage & Hérouard 1896. Alveolina, Cornuspira, Miliammina, Pyrgo, Quinqueloculina, Sorites.
    - Spirillinida Hohenegger & Piller 1975. Patellina, Spirillina.
    - Ammodiscidae Reuss 1862. Ammodiscus, Glomospira.
  - Globothalamea Pawlowski et al. 2012
    - Rotaliida Delage & Hérouard 1896
      - Planorbulinidae Schwager 1877. Planorbulinella, Hyalinea.
      - Discorboidea Ehrenberg 1838
        Discorbidae Ehrenberg 1838. Discorbis.
        
        Rosalinidae Reiss 1963. Rupertina, Discanomalina, "Rosalina", Gavelinopsis, Planorbulina.
      - Rotalioidea Ehrenberg 1839, emend. Pawlowski 2013. Incertae sedis genera: ?Criboelphidium, ?"Elphidium", ?Protelphidium.
        Elphidiidae Galloway 1933. Elphidium.
        
        Ammoniidae Saidova 1981. Ammonia.
        
        Elphidiellidae Holzmann & Pawlowski 2017. Elphidiella.
        
        Haynesinidae Mikhalevich 2013. Haynesina, Aubignyna.
      - Glabratelloidea Loeblich & Tappan 1964
        Rotaliellidae Loeblich & Tappan 1964. Rotaliella, Rossyatella.
        
        Buliminoididae Seiglie 1970. Buliminoides.
        
        Glabratellidae Loeblich & Tappan 1964. Glabratella, Glabratellina, Angulodiscorbis, Planoglabratella.
      - Calcarinoidea Schwager 1876
        Calcarinidae Schwager 1876. Neorotalia, Baculogypsina, Baculogypsinoides, Schlumbergerella, Pararotalia.
      - Nummulitoidea de Blainville 1827
        Nummulitidae de Blainville 1827. Nummulites, Operculinella, Cycloclypeus, Heterostegina, Operculina, Planoperculina, Planostegina.
      - Serioidea Holzmann & Pawlowski 2017
        Uvigerinidae Haeckel 1894. Uvigerina, Rectuvigerina, Trifarina.
        
        Bolivinitidae Glaessner 1937. Bolivina, Brizalina, Saidovina.
        
        Cassidulinidae d'Orbigny 1839. Globocassidulina, Cassidulinoides, Evolvocassidulina, Islandiella, Ehrenbergina
        
        Sphaeroidinidae Cushman 1927. Sphaeroidina.
        
        Globobuliminidae Cushman 1927. Globobulimina.
      - Incertae sedis Rotaliida families:
        ?Nonionidae Schultze 1854. Nonion, Nonionella, Nonionellina, Nonionoides.
        
        ?Virgulinellidae Loeblich & Tappan 1984. Virgulinella.
        
        ?Buliminidae Jones 1875. Bulimina.
        
        ?Epistominellidae Holzmann & Pawlowski 2017. Epistominella.
        
        ?Stainforthiidae Reiss 1963. Stainforthia, Gallitellia.
        
        ?Cibicididae Cushman 1927. Cibicides, Cibicidoides, Heterolepa.
        
        ?Chilostomellidae Brady 1881. Chilostomella.
        
        ?Pullenidae Schwager 1877. Pullenia.
        
        ?Nuttalidae Saidova 1981. Nuttalides.
        
        ?Discorbinellidae Sigal 1952. Discorbinella, Hanzawaia.
        
        ?Astrononionidae Cushman & Edwards 1937. Astrononion.
        
        ?Oridorsalidae Loeblich & Tappan 1984. Oridorsalis.
        
        ?Melonidae Holzmann & Pawlowski 2017. Melonis.
        
        ?Cymbaloporidae Cushman 1927. Cymbaloporella.
        
        ?Rubratelliidae Holzmann & Pawlowski 2017. Rubratella.
        
        ?Murrayinelliidae Holzmann & Pawlowski 2017. Murrayinella.
    - Globigerinida Lankester 1885 emend. Arz, Arenillas & Gilabert 2022^[7] (P)
      - †Parvularugoglobigerinoidea Arenillas, Arz & Gilabert 2022
        †Parvularuglobigerinidae Arenillas, Arz & Gilabert 2022. Pseudocaucasina, Palaeoglobigerina, Parvularugoglobigerina.
      - Eoglobigerinoidea BouDagher-Fadel 2012
        †Eoglobigerinidae Blow 1979. Alicantina, Eoclavatorella, Eoglobigerina, Parasubbotina, Pseudoglobigerinella, Subbotina, Turbeogloborotalia.
        
        Globoquadrinidae Blow 1979. Dentoglobigerina, Globoquadrina.
        
        †Neoacarininidae BouDagher-Fadel 2012. Neoacarinina.
        
        †Porticulasphaeridae Banner 1982. Globigerinatheka, Guembelitrioides, Inordinatosphaera, Orbulinoides, Porticulasphaera.
      - Globigerinoidea Carpenter, Parker & Jones 1862
        Globigerinidae Carpenter, Parker & Jones 1862. Alloglobigerinoides, Ciperoella, Globigerina, Globicuniculus, Globigerinoides, Globigerinoidesella, Globoturborotalita, Trilobigerina [Trilobatus], Zeaglobigerina.
        
        Globigerinellidae BouDagher-Fadel 2012. Beella, Bolliella, Globigerinella, Orcadia, Protentella, Quiltyella.
        
        Hastigerinidae Bolli, Loeblich & Tappan 1957. Hastigerina, Hastigerinella, Hastigerinopsis.
        
        Orbulinidae Schultze 1854. Biorbulina, Candorbulina, Orbulina, Praeorbulina.
        
        Sphaeroidinellidae Banner & Blow 1959. Prosphaeroidinella, Sphaeroidinella, Sphaeroidinellopsis.
        
        Turborotalitidae Hofker 1976. Berggrenia, Turborotalita.
      - Globorotalioidea Cushman 1927
        †Catapsydracidae Bolli, Loeblich & Tappan 1957. Catapsydrax, Globigerinopsoides, Globigerinoita, Velapertina.
        
        Globorotaloididae Banner & Blow 1959. Clavatorella, Globorotaloides, Protentelloides.
        
        Globorotaliidae Cushman 1927. Dentigloborotalia, Globoconella, Globorotalia, Hirsutella, Jenkinsella, Menardella, Neogloboquadrina, Paragloborotalia, Truncorotalia.
        
        Pulleniatinidae Cushman 1927. Pulleniatina.
      - †Globanomalinidoidea Loeblich & Tappan 1984
        †Globanomalinidae Loeblich & Tappan 1984. Carinoturborotalia, Globanomalina, Luterbacheria, Planoglobanomalina, Turborotalia.
      - †Hantkeninoidea Cushman 1927
        †Pseudohastigerinidae Canudo 1990. Pseudohastigerina.
        
        †Hantkeninidae Cushman 1927. Applinella, Aragonella, Clavigerinella, Cribrohantkenina, Hantkenina.
      - †Truncorotaloidinoidea BouDagher-Fadel 2012
        †Globigerapsidae Blow 1979. Globigerapsis, Muricoglobigerina.
        
        †Planorotalitidae BouDagher-Fadel 2012. Astrorotalia, Planorotalites.
        
        †Truncorotaloididae Loeblich & Tappan 1961. Acarinina, Igorina, Morozovella, Morozovelloides, Pearsonites, Praemurica, Pseudogloboquadrina, Testacarinata, Truncorotaloides.
    - †Globotruncanida Arz, Arenillas & Gilabert 2022^[7]
      - †Abathomphaloidea Arz, Arenillas & Gilabert 2022
        †Abathomphalidae Pessagno 1967. Abathomphalus.
        
        †Globotruncanellidae Maslakova 1964. Globotruncanella, Spinoglobotruncanella.
      - †Favuselloidea Longoria 1974
        †Conoglobigerinidae BouDagher-Fadel, Banner & Whittaker 1997. Conoglobigerina, Tenuigerina, ?Sphaerogerina.
        
        †Favusellidae Longoria 1974. Ascoliella, Favusella, Koutsoukosia.
        
        †Globuligerinidae Loeblich & Tappan 1984. Compactogerina, Globuligerina, Haeuslerina, Petaloglobigerina.
      - †Hedbergelloidea Longoria & Gamper 1975
        †Ananiidae El-Nakhal 2010. Anania, Badriella, Costellagerina, Hillsella, Liuenella [Liuella], Loeblichella, Muricohedbergella, Paracostellagerina, Pessagnoina, Planohedbergella, Pseudoclavihedbergella, Vanhintella.
        
        †Hedbergellidae Loeblich & Tappan 1961. Asterohedbergella, Clavihedbergella, Hedbergella, Microhedbergella, Paraticinella, Pseudoguembelitria.
        
        †Helvetoglobotruncanidae Lamolda 1976. Angulocarinella, Bermudeziana, Bollitruncana, Fingeria, Hedbergellita, Brittonella, Helvetoglobotruncana, Unitruncatus, Whiteinella.
        
        †Praehedbergellidae Banner & Desai 1988. Blefuscuiana, Gorbachikella, Praehedbergella, Lilliputianella, Lilliputianelloides, Wondersella.
      - †Globotruncanoidea Brotzen 1942
        †Globotruncanidae Brotzen 1942. Contusotruncana, Globotruncana, Marginotruncana, Obliquacarinata, Sphaerotruncana, Ventrotruncana.
        
        †Praeglobotruncanidae Ion 1983. Concavatotruncana, Dicarinella, Falsotruncana, Rotundina, Praeglobotruncana, Verotruncana.
        
        †Reissidae Korchagin 2001. Elevatotruncana, Globotruncanita, Kassabiana, Radotruncana, Sigalitruncana, Turbotruncana.
      - †Planomalinoidea Bolli, Loeblich & Tappan 1957
        †Eohastigerinellidae Loeblich & Tappan 1984. Eohastigerinella, Hastigerinoides.
        
        †Globigerinelloididae Longoria 1974. Alanlordella, Allotheca, Biglobigerinella, Blowiella, Claviblowiella, Globigerinelloides, Pseudoschackoina.
        
        †Planomalinidae Bolli, Loeblich & Tappan 1957. Bannerina, Planomalina, Pseudoplanomalina.
        
        †Schackoinidae Pokorný 1958. Asymetria, Groshenyia, Leupoldina, Neoschackoina, Schackoina.
      - †Rotaliporoidea Sigal 1958
        †Rotaliporidae Sigal 1958. Anaticinella, Pseudothalmanninella, Rotalipora, Thalmanninella.
        
        †Ticinellidae Longoria 1974. Biticinella, Claviticinella, Ticinella.
      - †Rugoglobigerinoidea Subbotina 1959
        †Helvetiellidae Longoria & Gamper 1984. Archaeoglobigerina, Bucherina, Dorbignya, Edgarinella, Gandolfia, Gansserina, Globocarinata, Helvetiella, Kuglerina.
        
        †Rugoglobigerinidae Subbotina 1959. Archaeoglobitruncana, Plummerita, Rugoglobigerina, Rugosocarinata, Rugotruncana, Trinitella.
    - †Heterohelicida Fursenko 1958, emend. Arz, Arenillas & Gilabert 2022^[7]
      - †Heterohelicoidea Cushman 1927
        †Gublerinidae Aliyulla 1977. Gublerina, Lipsonia, Praegublerina.
        
        †Heterohelicidae Cushman 1927. Braunella, Bronnimannella, Ehrenbergites, Globoheterohelix, Fleisherites, Hartella, Heterohelix, Huberella, Laeviheterohelix, Lazarusina, Lunatriella, Magellanina, Mihaia, Nederbragtina, Planoheterohelix, Protoheterohelix, Pseudoplanoglobulina, Steineckia, Striataella, Texasina, ?Bifarina, ?Rectoguembelina, ?Zeauvigerina.
        
        †Pseudotextulariidae Maamouri & Salaj 1978. Planoglobulina, Pseudotextularia, Racemiguembelina.
        
        †Pseudoguembelinidae Aliyulla 1977. Eicheriella, Leptobimodalia, Pseudoguembelina.
        
        †Spiroplectidae Cushman 1911. Hendersonites [Hendersonia], Neohendersonites, Paraspiroplecta, Spiroplecta.
        
        †Ventilabrellidae Maamouri & Salaj 1978. Planulitella, Proliferania, Sigalia, Ventilabrella.
    - †Guembelitriida Arenillas, Arz & Gilabert 2022^[7]
      - †Cassigerinelloidea Bolli, Loeblich & Tappan 1957
        †Cassigerinellidae Bolli, Loeblich & Tappan 1957. Cassigerinella, Riveroinella.
      - †Guembelitrioidea Montanaro-Gallitelli 1957
        †Guembelitriidae Montanaro-Gallitelli 1957. Cassigerinelloita, Guembelitria, Chiloguembelitria, Jenkinsina, ?Archaeoguembelitria, ?Gallitellia, ?Guembelitriella.
      - †Chiloguembelinoidea Reiss 1963
        †Chiloguembelinidae Reiss 1963. Chiloguembelina, Woodringina, ?Streptochilus.
      - †Globoconusoidea BouDagher-Fadel 2012
        †Globoconusidae BouDagher-Fadel 2012. Globoconusa, Trochoguembelitria,
    - Order ? (unnamed)^[7]
      - Globigerinitoidea BouDagher-Fadel 2012, emend. Arenillas, Arz & Gilabert 2022^[7]
        Candeinidae Cushman 1927. Candeina.
        
        †Globigerinatellidae BouDagher-Fadel 2012. Globigerinatella.
        
        Globigerinitidae Bermúdez 1961. Globigerinita, Mutabella, Polyperibola, Tinophodella.
        
        Tenuitellidae BouDagher-Fadel 2012. Praetenuitella, Tenuitella, Tenuitellinata, Tenuitellita.
        
        †Family ? (unnamed). Dipsidripella, ?Antarcticella.
    - Robertinida Loeblich & Tappan 1984. Hoeglundina, Robertina, Robertinoides.
    - Textulariida Delage & Hérouard 1896 (P). Cyclammina, Eggerella, Reophax, Textularia, Trochammina.
    - Carterinida Loeblich & Tappan 1981. Carterina.
- Radiolaria Müller 1858, sensu Adl et al. 2005
  - Acantharea Haeckel 1881, emend. Mikrjukov 2000
    - Chaunocanthida Schewiakoff 1926. Amphiacon, Conacon, Gigartacon, Heteracon, Stauracon.
    - Holocanthida Schewiakoff 1926. Acanthochiasma, Acanthocolla, Acanthoplegma.
    - Symphyacanthida Schewiakoff 1926. Amphilithium, Astrolonche, Pseudolithium.
    - Arthracanthida Schewiakoff 1926. Acanthometra, Daurataspis, Dictyacantha, Diploconus, Phractopelta, Phyllostaurus, Pleuraspis, Stauracantha.
  - Taxopodida Fol 1883. Sticholonche.
  - Polycystinea Ehrenberg 1838, emend. Haeckel 1887
    - Spumellaria Ehrenberg 1875, Haeckel 1887, emend. Riedel 1967. Actinomma, Didymocyrtis, Euchitonia, Hexacontium, Hexalonche, Hexastylus, Octodendron, Plegmosphaera, Saturnalis, Spongaster, Spongosphaera.
    - Nassellaria Ehrenberg 1875, emend. Haeckel 1887. Artostrobus, Eucyrtidium, Lithomelissa, Pterocanium, Pterocorys.
    - Collodaria Haeckel 1887. Acrosphaera, Collosphaera, Collozoum, Sphaerozoum, Rhaphidozoum, Siphonsphaera, Thalassicolla.
    - Orodaria Nakamura & Suzuki 2020^[68]
      - Oroscenidae Haeckel 1887 emend. Nakamura & Suzuki 2021 [Orosphaerida Haeckel 1887; Orosphaeridae Haecker 1908]. Oroscena, Orostaurus, Oropelex. Nomina dubia genera: Orosphaera, Orodictyum, Orona, Oronium.
      - Thalassothamnidae Haecker 1906 emend. Nakamura & Suzuki 2021 [Cytocladidae Schröder, 1908]. Thalassothamnus, Cytocladus, ?Triassothamnus†. Nomen dubium genus: Conostylus.
Aquavolonida Bass & Berney 2018. Aquavolon, Lapot gusevi.^[49]
Tremulida Howe et al. 2011. Tremula.

Haptista Cavalier-Smith 2003

Haptophyta Hibberd 1976, ex. Edvardsen & Eikrem 2000
- Pavlovales Green 1976 [Pavlovophyceae Cavalier-Smith 1986]. Diacronema, Exanthemachrysis, Pavlova, Rebecca.
- Prymnesiophyceae Hibberd 1976
  - Prymnesiales Papenfuss 1955, emend. Edvardsen & Eikrem 2000. Chrysochromulina, Chrysocampanula, Dicrateria, Haptolina, Prymnesium, Pseudohaptolina.
  - Phaeocystales Medlin 2000. Phaeocystis.
  - Isochrysidales Pascher 1910, emend. Edvardsen & Eikrem 2000. Emiliania, Gephyrocapsa, Isochrysis, Ruttnera, Tisochrysis.
  - Coccolithales Schwarz 1932, emend. Edvardsen & Eikrem 2000. Balaniger, Calciosolenia, Coccolithus, Hymenomonas, Chrysotila, Wigwamma.
- Rappephyceae M. Kawachi, R. Kamikawa & T. Nakayama 2021^[69]
  - Pavlomulinales M. Kawachi & I. Inouye 2021. Pavlomulina.
Centroplasthelida Febvre-Chevalier & Febvre 1984 [Centrohelea Kühn 1926 sensu Cavalier-Smith in Yabuki et al. 2012; Centroheliozoa Dürrschmidt & Patterson 1987]
- ?Parasphaerastrum.
- ?Spiculophryidae Shishkin & Zlatogursky 2018. Spiculophrys.
- Pterocystida Cavalier-Smith and von der Heyden 2007, emend. Shishkin and Zlatogursky 2018
  - Raphidista Shishkin & Zlatogursky 2018
    - Choanocystidae Cavalier-Smith & von der Heyden 2007. Choanocystis.
    - Raphidiophryidae Febvre-Chevalier & Febvre 1984, emend. Shishkin & Zlatogursky 2018. Raphidiophrys.
  - Pterista Shishkin & Zlatogursky 2018
    - Oxnerellidae Cavalier-Smith & Chao 2012. Oxnerella.
    - Pterocystidae Cavalier-Smith & von der Heyden 2007. Pterocystis, Raineriophrys, Chlamydaster, Pseudoraphidiophrys, Pseudoraphidocystis.
    - Heterophryidae Poche 1913, emend. Cavalier-Smith & von der Heyden 2007. Heterophrys, Sphaerastrum.
- Panacanthocystida Shishkin & Zlatogursky 2018
  - Yogsothothidae Shishkin & Zlatogursky 2018 [Chthonida Shishkin & Zlatogursky 2018; Yogsothothina Shishkin & Zlatogursky 2018]. Yogsothoth.
  - Acanthocystida Cavalier-Smith & von der Heyden 2007 emend. Shishkin & Zlatogursky 2018
    - Marophryidae Cavalier-Smith & von der Heyden 2007 emend. Shishkin & Zlatogursky 2018 [Marophryina Cavalier-Smith in Yabuki et al. 2012]. Marophrys.
    - Chalarothoracina Hertwig & Lesser 1874 sensu Cavalier-Smith in Yabuki et al. 2012 emend. Shishkin & Zlatogursky 2018
      - Acanthocystidae Claus 1874 emend. Shishkin & Zlatogursky 2018. Acanthocystis.
      - Raphidocystidae Zlatogursky 2018. Raphidocystis.

Cryptista Cavalier-Smith 1989, 2018, emend. Adl et al. 2019

Palpitomonas bilix Yabuki & Ishida 2010
Cryptophyceae Pascher 1913, emend. Schoenichen 1925, emend. Adl et al. 2012 [Cryptophyta Silva 1962; Cryptophyta Cavalier-Smith 1986]
- ?Bjornbergiella Bicudo 1965
- Cryptomonadales Pascher 1913. Chroomonas, Cryptomonas, Falcomonas, Geminigera, Guillardia, Hanusia, Hemiselmis, Plagioselmis, Proteomonas, Rhinomonas, Rhodomonas, Storeatula, Teleaulax.
- Cyathomonadacea Pringsheim 1944. Goniomonas [previously Cyathomonas], Hemiarma.
- Kathablepharidacea Skuja 1939 [Kathablepharidae Vørs 1992; Leucocryptea Cavalier-Smith 2004]. Hatena, Kathablepharis, Leucocryptos, Platychilomonas, Roombia.

Incertae sedis Eukarya

Meteora sporadica Hausmann, Weitere, Wolf & Arndt, 2002^[70]

Hemimastigophora Foissner et al. 1988

Spironemidae Doflein 1916. Hemimastix, Spironema, Stereonema.
Spironematellidae Shshkin 2022. Spironematella.^[71]
?Paramastix Skuja 1948

Excavates (P)

Malawimonadida Cavalier-Smith 2003

Malawimonadidae O' Kelly & Nerad 1999. Gefionella, Malawimonas.
Imasidae Heiss, Simpson, & Kim 2020. Imasa.^[72]

Metamonada Grassé 1952, emend. Cavalier-Smith 1987

?Barthelona
Anaeramoebae^[73] [Anaeramoebidae Táborský, Pánek & Čepička 2017]. Anaeramoeba.^[74]
Fornicata Simpson 2003
- "Carpediemonas-like organisms" (Kolisko et al. 2010) (P). Aduncisulcus, Carpediemonas, Dysnectes, Ergobibamus, Hicanonectes, Kipferlia.
- Diplomonadida Wenyon 1926
  - Hexamitinae Kent 1880. Enteromonas, Gyromonas*, Hexamita, Spironucleus, Trepomonas, Trigonomonas*, Trimitus.
  - Giardiinae Kulda & Nohýnková 1978. Brugerolleia*, Giardia, Octomitus.
- Retortamonadida Grassé 1952 (P). Chilomastix, Retortamonas.
- Caviomonadidae Cavalier-Smith 2013. Caviomonas*, Iotanema.
Parabasalia Honigberg 1973
- ?Tricercomitus
- Trichomonadida Kirby 1947. Cochlosoma, Dientamoeba, Lacusteria, Pentatrichomonas, Pentatrichomonoides, Pseudotrichomonas, Pseudotrypanosoma, Tetratrichomonas, Trichomonas, Trichomonoides, Trichomitopsis.
- Honigbergiellida Čepička et al. 2010 (P?). Ditrichomonas, Cthulhu, Cthylla, Hexamastix, Honigbergiella, Monotrichomonas.
- Hypotrichomonadida Čepička et al. 2010. Hypotrichomonas, Trichomitus.
- Tritrichomonadida Čepička et al. 2010 (P?). Dientamoeba, Histomonas, Monocercomonas, Parahistomonas, Simplicimonas, Tritrichomonas.
- Cristamonadida Brugerolle & Patterson 2001. Caduceia, Calonympha, Coronympha, Deltotrichonympha, Devescovina, Foaina, Gigantomonas, Joenia, Joenina, Joenoides, Joenopsis*, Kofoidia, Koruga, Macrotrichomonas, Macrotrichomonoides, Metadevescovina, Mixotricha, Pachyjoenia*, Projoenia*, Pseudodevescovina, Rhizonympha*, Snyderella, Stephanonympha.
- Spirotrichonymphida Grassé 1952. Holomastigotes*, Holomastigotoides, Microjoenia*, Micromastigotes*, Rostronympha*, Spiromastigotes*, Spironympha*, Spirotrichonympha*, Spirotrichonymphella, Uteronympha*.
- Lophomonadida Light 1927. Lophomonas.
- Trichonymphida Poche 1913. Barbulanympha, Eucomonympha, Heliconympha, Hoplonympha, Leptospironympha, Macrospironympha*, Pseudotrichonympha, Rhynchonympha*, Spirotrichosoma*, Staurojoenina, Teranympha, Trichonympha, Urinympha.
Preaxostyla Simpson 2003
- Oxymonadida Grassé 1952. Barroella, Blattamonas, Brachymonas, Dinenympha, Microrhopalodina, Monocercomonoides, Notila, Opisthomitus, Oxymonas, Paranotila, Polymastix, Pyrsonympha, Sauromonas, Saccinobaculus, Streblomastix, Tubulimonoides.
- Trimastigidae Saville Kent 1880-1882. Trimastix.
- Paratrimastigidae Zhang et al. 2015. Paratrimastix.

Discoba Simpson in Hampl et al. 2009

Jakobida Cavalier-Smith 1993
- Ophirinina Yabuki, Gyaltshen, Heiss & Kim 2018^[75]
  - Agogonidae Galindo, Prokina, Torruella, López-García & Moreira 2022. Agogonia.^[76]
  - Ophirinidae Yabuki, Gyaltshen, Heiss & Kim 2018. Ophirina.
- Andalucina Cavalier-Smith 2013
  - Andaluciidae Cavalier-Smith 2013. Andalucia.
  - Stygiellidae Pánek, Táborský & Čepička 2015.^[77] Stygiella, Velundella.
- Histionina Cavalier-Smith 2013. Histiona, Jakoba, Moramonas, Reclinomonas, Seculamonas nomen nudum.
Tsukubamonadida Yabuki et al. 2011. Tsukubamonas.
Heterolobosea Page & Blanton 1985 [Percolozoa Cavalier-Smith 1991]
- Pharyngomonada Cavalier-Smith 2008. Pharyngomonas
- Tetramitia Cavalier-Smith 1993
  - Selenaionidae Hanousková et al. 2018. Dactylomonas, Selenaion.
  - Neovahlkampfiidae Hanousková et al. 2018. Neovahlkampfia.
  - Eutetramitia Hanousková et al. 2018
    - Vahlkampfiidae Jollos 1917 (P). Fumarolamoeba, Heteramoeba, Naegleria, Neovahlkampfia, Paravahlkampfia, Tetramitus, Vahlkampfia, Willaertia.
    - Gruberellidae Page & Blanton 1985. Gruberella*, Stachyamoeba.
    - Acrasidae Poche 1913. Acrasis, Allovahlkampfia, Pocheina.
    - Percolomonadidae Cavalier-Smith 2008. Percolomonas.
    - Psalteriomonadidae Cavalier-Smith 1993. Harpagon, Psalteriomonas, Monopylocystis, Pseudoharpagon, Sawyeria.
    - Stephanopogonidae Corliss 1961. Stephanopogon.
  - Creneidae Pánek et al. 2014. Creneis.
  - Tulamoebidae Kirby et al. 2015. Pleurostomum, Tulamoeba.
Euglenozoa Cavalier-Smith 1981, emend. Simpson 1997
- Euglenida Butschli 1884, emend. Simpson 1997
  - Heteronematina Leedale 1967 (P)^{[lower-alpha 19]}. Anisonema, Atraktomonas, Biundula, Calycimonas, Decastava, Dolium, Dinema, Dylakosoma, Entosiphon, Heteronema, Jenningsia, Keelungia, Lentomonas, Neometanema, Notosolenus, Pentamonas, Peranema, Peranemopsis, Petalomonas, Ploeotia, Scytomonas, Serpenomonas, Sphenomonas, Teloprocta, Tropidoscyphus, Urceolus.
  - Aphagea Cavalier-Smith 1993, emend. Busse & Preisfeld 2002. Astasia sensu stricto, Distigma, Gyropaigne, Menoidium, Parmidium, Rhabdomonas.
  - Euglenophyceae Schoenichen 1925, emend. Marin & Melkonian 2003 [Euglenea Butschli 1884, emend. Busse & Preisfeld 2002]
    - Rapaza Yamaguchi et al. 2012
    - Eutreptiales Leedale 1967, emend. Marin & Melkonian 2003. Eutreptia, Eutreptiella.
    - Euglenales Leedale 1967, emend. Marin & Melkonian 2003
      - Phacaceae Kim et al. 2010. Discoplastis, Lepocinclis, Phacus.
      - Euglenaceae Dujardin 1841, emend. Kim et al. 2010. Ascoglena, Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenamorpha, Euglenaria, Euglenopsis, Hegneria, Klebsina, Monomorphina, Strombomonas, Trachelomonas.
- Diplonemea Cavalier-Smith 1993, emend. Simpson 1997
  - Diplonemidae Cavalier-Smith 1993, emend. Adl et al. 2019. Diplonema, Rhynchopus, Lacrimia, Sulcionema, Flectonema.
  - Hemistasiidae Cavalier-Smith 2016, emend. Adl et al. 2019. Hemistasia.
  - Eupelagonemidae Okamoto & Keeling 2018. Eupelagonema.
- Symbiontida Yubuki et al. 2009. Bihospites, Calkinsia, Postgaardi.
- Kinetoplastea Honigberg 1963. Incertae sedis genera: ?Bordnamonas, ?Cephalothamnium, ?Rhynchoidomonas.
  - Prokinetoplastina Vickerman in Moreira et al. 2004. Ichthyobodo, Perkinsela.
  - Metakinetoplastina Vickerman in Moreira et al. 2004
    - Neobodonida Vickerman in Moreira et al. 2004. Actuariola, Avlakibodo,^[78] Azumiobodo, Cruzella, Cryptaulax, Dimastigella, Klosteria, Neobodo, Phanerobia, Rhynchobodo, Rhynchomonas.
    - Parabodonida Vickerman in Moreira et al. 2004. Cryptobia, Jarrellia, Parabodo, Procryptobia, Trypanoplasma.
    - Eubodonida Vickerman in Moreira et al. 2004. Bodo.
    - Trypanosomatida Kent 1880, emend. Vickerman in Moreira et al. 2004. Angomonas, Blechomonas, Leptomonas, Paratrypanosoma, Sergeia, Strigomonas, Wallaceina, Phytomonas, Trypanosoma.
      - Leishmaniinae Maslov & Lukeš 2012. Borovskyia, Crithidia, Leptomonas, Lotmaria, Novymonas, Porcisia, Zelonia, Endotrypanum, Leishmania.

Clades basal to Amorphea

CRuMs Brown et al. 2018 [Varisulca Cavalier-Smith 2013 emend. 2021; Crumalia Zmitr., Perelygin & Zharikov 2022]
- Collodictyonidae Brugerolle et al. 2002, emend. Adl et al. 2019 [Diphylleidae Cavalier-Smith 1993; Diphylleida Cavalier-Smith 1993; Diphyllatea Cavalier-Smith 2003, Sulcomonadidae Cavalier-Smith 2013]. Collodictyon, Diphylleia [Aulacomonas], Sulcomonas.
- Rigifilida Cavalier-Smith in Yabuki et al. 2012 [Hilomonadea Cavalier-Smith 2008 emend. 2012]. Micronuclearia, Rigifila.
- Mantamonadida Cavalier-Smith in Glücksman et al. 2011 [Glissodiscea Cavalier-Smith 2013 emend. 2021]. Mantamonas.
Ancyromonadida Cavalier-Smith 1998 [Planomonadida Cavalier-Smith 2008; Planomonadea Cavalier-Smith 2021; Planomonada Cavalier-Smith 2021]. Ancyromonas, Fabomonas, Nutomonas, Planomonas.

Genera of uncertain affiliation

Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Anaeramoeba, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol,^[79] Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium^{[lower-alpha 20]}, Copromonas, Cyanomastix, Cyclomonas, Cytamoeba, Dallingeria, Dictyomyxa, Dimastigamoeba, Dinemula, Dinoasteromonas, Diplocalium, Diplomita, Diplophysalis, Diploselmis, Dobellina, Ducelleria, Ectobiella, Elaeorhanis, Embryocola, Endamoeba, Endemosarca, Endobiella, Endomonas, Endospora, Enteromyxa, Eperythrocytozoon, Errera, Fromentella, Gweamonas,^[80] Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Lagenidiopsis, Liegeosia, Luffisphaera^{[lower-alpha 21]}, Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Meringosphaera, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon^{[lower-alpha 22]}, Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Piridium, Pleuophrys, Pleuromastix, Protenterospora, Protomonas, Pseudoactiniscus, Pseudosporopsis, Rhizomonas, Rhynchodinium, Rigidomastix, Schewiakoffia, Sergentella, Serpentoplasma, Sphaerasuctans, Spongastericus, Spongocyclia, Stephanomonas, Strobilomonas, Tetradimorpha, Tetragonidium, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.^[3]

Notes

↑ The first eukaryotes were “neither plants, animals, nor fungi”, hence as defined, the Protista would include the earliest common ancestor of all eukaryotes.
↑ In the original 4-kingdom model proposed in 1959, Protista included all unicellular microorganisms such as bacteria.
1 2 3 There are two competing phylogenetic hypotheses: Teretosporea (Corallochytrium + Ichthyosporea) and Pluriformea (Corallochytrium + Syssomonas).^[3] This article follows the latter hypothesis, because it is strongly supported by the most recent phylogenetic studies.^[11]
↑ The term "Choanozoa" has been used since 1991 by Cavalier-Smith as a paraphyletic assemblage of opisthokont protists, and the terms "Apoikozoa" and "choanimal" were proposed as names for the clade Metazoa+Choanoflagellata. However, these terms have not been formally described or adopted, and were rejected in favour of a renamed Choanozoa to fit the clade Metazoa+Choanoflagellata.^[3]
↑ The position of the genera Microcorycia, Parmulina, Penardochlamys and Zonomyxa, which were listed in 2002 under family Microcoryciidae, is not clear. They are placed here by morphological characters but this needs to be supported by molecular data.^[3]
↑ The latest revision by Adl et al. (2019) ignores the grouping of some variosean genera into higher rank clades that was made in older studies because of the weakly supported SSU phylogenetic analyses, except for Fractovitellida, which is fully supported by phylogenomic analyses from 2017.^[3]
1 2 3 4 5 6 7 This order was initially divided into families, but phylogenetic analyses haven't supported the monophyly of each family. For this reason, in recent classifications there is no family rank division within it.^[19]^[3]
↑ This genus groups with Dermamoebidae in a phylogenetic anaysis that uses a limited number of taxa.^[25] In the recent taxonomy it is listed as a separate clade until its position is better resolved.^[3]
↑ This genus could be a synonym of Vannella.^[3]
↑ Both genera group together in some phylogenetic analyses, but usually appear separated. They are considered a potential branch of Discosea, unless proven otherwise in the future with better taxon sampling.^[3]
↑ Latest analyses show that Microheliella is the sister group to Cryptista.^[12]
↑ Telonemia is the sister group to the SAR clade.^[9]
↑ The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.^[31]
↑ Cavalier-Smith and Scoble (2013) show a sister relationship between raphidophytes and Actinophryida.^[42]
↑ Highly divergent 18S rRNA.^[3]
↑ This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.^[3]
1 2 Initially, Cercozoa contained the clades Filosa and Endomyxa; however it has recently been synonymized with Filosa after a study found Endomyxa more closely related to Retaria.^[48] The current classification places Endomyxa either as the sister clade of Retaria or as part of Retaria, even though more recent studies support the monophyly of Cercozoa as Filosa+Endomyxa again.^[49]
↑ There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.^[3]
↑ There is no phylogenetic taxonomy for phagotrophic euglenids. Some possibly monophyletic taxa have been proposed that cover restricted subgroups of the phagotrophic euglenids, such as Ploeotiida (Ploeotia, Entosiphon, Lentomonas, and presumably Keelungia) and Petalomonadida (Petalomonas, Notosolenus and Calycimonas, and presumably also taxa such as Sphenomonas). There is a limited taxon sampling for molecular data, and many traditional genera are probably paraphyletic.^[3]
↑ Probably a synonym of the zygomycete fungus Nephridiophaga.^[3]
↑ May be the same genus as Belonocystis.^[3]
↑ It is not yet known whether this organism is an eukaryote or a prokaryote.^[81]

References

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↑ Blandenier Q, Seppey CVW, Singer D, Vlimant M, Simon A, Duckert C, Lara E (2016). "Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle" (PDF). Journal of Eukaryotic Microbiology. 64 (2): 257–265. doi:10.1111/jeu.12357. PMID 27543384. S2CID 4665573.
↑ Kudryavtsev, Alexander; Voytinsky, Fyodor; Volkova, Ekaterina (July 2022). "Coronamoeba villafranca gen. nov. sp. nov. (Amoebozoa, Dermamoebida) challenges the correlation of morphology and phylogeny in Amoebozoa". Scientific Reports. 12 (1): 12541. Bibcode:2022NatSR..1212541K. doi:10.1038/s41598-022-16721-2. PMC 9307759. PMID 35869259.
↑ Melton JT, Wood FC, Branch J, Singla M, Tekle YI (2019). "Phylogenomics of Thecamoebida (Discosea, Amoebozoa) with the Description of Stratorugosa tubuloviscum gen. nov. sp. nov., a Freshwater Amoeba with a Perinuclear MTOC". Protist. 170 (1): 8–20. doi:10.1016/j.protis.2018.09.002. ISSN 1434-4610. PMID 30553127. S2CID 56174714.
↑ Mesentsev Y, Bondarenko N, Kamyshatskaya O, Nassonova E, Glotova A, Loiko S, Istigechev G, Kulemzina A, Abakumov E, Rayko M, Lapidus A, Smirnov A (2023). "Thecochaos is not a myth: study of the genus Thecochaos (Amoebozoa, Discosea) – a rediscovered group of lobose amoeba, with short SSU gene". Organisms Diversity & Evolution. 23: 7–24. doi:10.1007/s13127-022-00581-9. S2CID 251658030.
↑ Tice AK, Shadwick LL, Fiore-Donno AM, et al. (2016). "Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group". Biol Direct. 11 (1): 69. doi:10.1186/s13062-016-0171-0. PMC 5192571. PMID 28031045.
↑ Tikhonenkov DV, Jamy M, Borodina AS, Belyaev AO, Zagumyonnyi DG, Prokina KI, Mylnikov AP, Burki F, Karpov SA (2022). "On the origin of TSAR: morphology, diversity and phylogeny of Telonemia". Open Biology. 12 (3): 210325. doi:10.1098/rsob.210325. PMC 8924772. PMID 35291881.
↑ Schön ME, Zlatogursky VV, Singh RP, et al. (2021). "Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae". Nat Commun. 12 (1): 6651. Bibcode:2021NatCo..12.6651S. doi:10.1038/s41467-021-26918-0. PMC 8599508. PMID 34789758.
↑ Gawryluk, Ryan M. R.; Tikhonenkov, Denis V.; Hehenberger, Elisabeth; Husnik, Filip; Mylnikov, Alexander P.; Keeling, Patrick J. (August 2019). "Non-photosynthetic predators are sister to red algae". Nature. 572 (7768): 240–243. doi:10.1038/s41586-019-1398-6. ISSN 1476-4687. PMID 31316212. S2CID 197542583.
↑ Weston EJ, Eglit Y, Simpson AGB (2023). "Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles". Journal of Eukaryotic Microbiology. 00: e13003. doi:10.1111/jeu.13003.
↑ Rybarski AE, Nitsche F, Park JS, Filz P, Schmidt P, Kondo R, Simpson AGB, Arndt H (2021). "Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments". European Journal of Protistology. 81: 125809. doi:10.1016/j.ejop.2021.125809. ISSN 0932-4739. PMID 34673437. S2CID 236377023.
↑ Jirsová D, Füssy Z, Richtová J, Gruber A, Oborník M (2019). "Morphology, Ultrastructure, and Mitochondrial Genome of the Marine Non-Photosynthetic Bicosoecid Cafileria marina Gen. et sp. nov". Microorganisms. 7 (8): 240. doi:10.3390/microorganisms7080240. PMC 6723347. PMID 31387253.
↑ Harder, Christoffer Bugge; Ekelund, Flemming; Karpov, Sergey A. (March 2014). "Ultrastructure and phylogenetic position of Regin rotiferus and Otto terricolus genera et species novae (Bicosoecida, Heterokonta/Stramenopiles)". Protist. 165 (2): 144–160. doi:10.1016/j.protis.2014.01.004. PMID 24637333.
↑ Hassett, Brandon T. (2020). "A Widely Distributed Thraustochytrid Parasite of Diatoms Isolated from the Arctic Represents a gen. and sp. nov". Journal of Eukaryotic Microbiology. International Society of Protistologists. 67 (4): 480–490. doi:10.1111/jeu.12796. hdl:10037/19021. PMID 32249965.
↑ Shiratori, Takashi; Thakur, Rabindra; Ishida, Ken-ichiro (2017). "Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a Poorly Studied Phagotrophic Biflagellate is the First Characterized Member of Stramenopile Environmental Clade MAST-6". Protist. 168 (4): 439–451. doi:10.1016/j.protis.2017.06.004. ISSN 1434-4610. PMID 28822908.
↑ Dovilė Barcytė; Wenche Eikrem; Anette Engesmo; Sergio Seoane; Jens Wohlmann; Aleš Horák; Tatiana Yurchenko; Marek Eliáš (2 March 2021). "Olisthodiscus represents a new class of Ochrophyta". Journal of Phycology. 57 (4): 1094–1118. doi:10.1111/jpy.13155. hdl:10852/86515. PMID 33655496.
↑ Amaral R, Fawley KP, Němcová Y, Ševčíková T, Lukešová A, Fawley MW, Santos LMA, Eliáš M (2020). "Toward Modern Classification of Eustigmatophytes, Including the Description of Neomonodaceae Fam. Nov. and Three New Genera". Journal of Phycology. 56 (3): 630–648. doi:10.1111/jpy.12980. PMC 7987219. PMID 32068883.
↑ Cavalier-Smith, Thomas (2017). "Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences". Protoplasma. 255 (1): 297–357. doi:10.1007/s00709-017-1147-3. PMC 5756292. PMID 28875267.
↑ Cavalier-Smith, Thomas; Scoble, Josephine Margaret (2013). "Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes". European Journal of Protistology. 49 (3): 328–353. doi:10.1016/j.ejop.2012.09.002. PMID 23219323.
↑ Wetherbee R, Jackson CJ, Repetti SI, Clementson LA, Costa JF, van de Meene A, Crawford S, Verbruggen H (April 2019). "The golden paradox - a new heterokont lineage with chloroplasts surrounded by two membranes". J Phycol. 55 (2): 257–278. doi:10.1111/jpy.12822. hdl:11343/233613. PMID 30536815. S2CID 54477112.
↑ Graf L, Yang EC, Han KY, Küpper FC, Benes KM, Oyadomari JK, Herbert RJH, Verbruggen H, Wetherbee R, Andersen RA, Yoon HS (December 2020). "Multigene Phylogeny, Morphological Observation and Re-examination of the Literature Lead to the Description of the Phaeosacciophyceae Classis Nova and Four New Species of the Heterokontophyta SI Clade". Protist. 171 (6): 125781. doi:10.1016/j.protis.2020.125781. PMID 33278705. S2CID 227315556.
↑ Bente Edvardsen; Wenche Eikrem; Kamran Shalchian-Tabrizi; Ingvild Riisberg; Geir Johnsen; Lars Naustvoll; Jahn Throndsen (15 September 2007). "Verrucophora farcimen gen. et sp. nov. (Dictyochophyceae, Heterokonta)—a bloom-forming ichthyotoxic flagellate from the Skagerrak, Norway". Journal of Phycology. 43 (5): 1054–1070. doi:10.1111/j.1529-8817.2007.00390.x. hdl:10852/11590.
↑ Han, Kwi Young; Graf, Louis; Reyes, Carolina P.; Melkonian, Barbara; Andersen, Robert A.; Yoon, Hwan Su; Melkonian, Michael (2018). "A Re-investigation of Sarcinochrysis marina (Sarcinochrysidales, Pelagophyceae) from its Type Locality and the Descriptions of Arachnochrysis, Pelagospilus, Sargassococcus and Sungminbooa genera nov". Protist. 169 (1): 79–106. doi:10.1016/j.protis.2017.12.004. ISSN 1434-4610. PMID 29427838.
↑ Weiss, James; Andreou, Demetra; Esteban, Genoveva F. (2022). "The Extraordinarily Rare Ciliate Legendrea loyezae Fauré-Fremiet, 1908 (Haptoria, Ciliophora)". Protist. 173 (6): 125912. doi:10.1016/j.protis.2022.125912. PMID 36242851.
1 2 Cavalier-Smith, Thomas; Chao, Ema E.; Lewis, Rhodri (April 2018). "Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria". Protoplasma. 255 (5): 1517–1574. doi:10.1007/s00709-018-1241-1. PMC 6133090. PMID 29666938.
1 2 Irwin, Nicholas A.T.; Tikhonenkov, Denis V.; Hehenberger, Elisabeth; Mylnikov, Alexander P.; Burki, Fabien; Keeling, Patrick J. (2019-01-01). "Phylogenomics supports the monophyly of the Cercozoa". Molecular Phylogenetics and Evolution. 130: 416–423. doi:10.1016/j.ympev.2018.09.004. ISSN 1055-7903. PMID 30318266. S2CID 52982396.
↑ Feng, Jian-Ju; He, Chen-Yang; Jiang, Shu-Hua; Zhang, Tao; Yu, Li-Yan (2021). "Saccharomycomorpha psychra n. g., n. sp., a Novel Member of Glissmonadida (Cercozoa) Isolated from Arctic and Antarctica". Journal of Eukaryotic Microbiology. 68 (3): e12840. doi:10.1111/jeu.12840. PMID 33448091.
↑ Dumack K, Pundt J, Bonkowski M (2020). "Transfer of the Thecate Amoeba Lecythium mutabilis to a Novel Genus Omnivora (Fiscullidae, Thecofilosea, Cercozoa)". J. Eukaryot. Microbiol. 67 (2): 245–251. doi:10.1111/jeu.12778. PMID 31808200. S2CID 208768245.
↑ Dumack K, Duckert C, Meinhardt R, Lara E, Bonkowski M (2021). "Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria, Cercozoa, Euglyphida) Sheds Light on Euglyphida's Dark Matter". J. Eukaryot. Microbiol. 68 (2): e12835. doi:10.1111/jeu.12835. hdl:10261/255052. PMID 33222324. S2CID 227135214.
↑ Siemensma F, Dumack K (2020). "SSU rDNA Phylogeny Indicates the Scale-lacking Trivalvulariida ord. nov. as a Sister Group to the Euglyphida (Cercozoa, Rhizaria)". Protist. 171 (1): 125701. doi:10.1016/j.protis.2019.125701. ISSN 1434-4610. PMID 31955058. S2CID 210829787.
↑ Bass D, Chao EE, Nikolaev S, Yabuki A, Ishida KI, Berney C, Pakzad U, Wylezich C, Cavalier-Smith T (2009). "Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised". Protist. 160 (1): 75–109. doi:10.1016/j.protis.2008.07.002. ISSN 1434-4610. PMID 18952499.
↑ Hess S, Suthaus A (2022). "The Vampyrellid Amoebae (Vampyrellida, Rhizaria)". Protist. 173 (1): 125854. doi:10.1016/j.protis.2021.125854. PMID 35091168. S2CID 245303468.
↑ Suthaus A, Hess S (2023). "Pseudovampyrella gen. nov.: A genus of Vampyrella-like protoplast extractors finds its place in the Leptophryidae". The Journal of Eukaryotic Microbiology. International Society of Protistologists. 00: e13002. doi:10.1111/jeu.13002.
↑ Kolátková V, Čepička I, Hoffman R, et al. (2021). "Marinomyxa Gen. Nov. Accommodates Gall-Forming Parasites of the Tropical to Subtropical Seagrass Genus Halophila and Constitutes a Novel Deep-Branching Lineage Within Phytomyxea (Rhizaria: Endomyxa)". Microb Ecol. 81 (3): 673–686. doi:10.1007/s00248-020-01615-5. PMID 33021677. S2CID 222148939.
↑ Engler A (1903). Syllabus der Pflanzenfamilien: eine Übersicht über das gesamte Pflanzensystem mit Berücksichtigung der Medicinal- und Nutzpflanzen nebst einer Übersicht über die Florenreiche und Florengebiete der Erde zum Gebrauch bei Vorlesungen und Studien über specielle und medicinisch-pharmaceutische Botanik (3rd ed.). Berlin: Borntraeger. doi:10.5962/bhl.title.22956.
↑ Neuhauser S, Kirchmair M, Bulman S, et al. (23 February 2014). "Cross-kingdom host shifts of phytomyxid parasites". BMC Evol Biol. 14 (33): 33. doi:10.1186/1471-2148-14-33. PMC 4016497. PMID 24559266.
↑ Sparrow FK (1960). Aquatic Phycomycetes. University of Michigan studies, Scientific series, v. 15. Ann Arbor, University of Michigan Press. doi:10.5962/bhl.title.5685. LCCN 59011269. OCLC 1362167.
↑ Dick, Michael W. (2001). Straminipilous Fungi: Systematics of the Peronosporomycetes Including Accounts of the Marine Straminipilous Protists, the Plasmodiophorids and Similar Organisms (1 ed.). Springer Dordrecht. doi:10.1007/978-94-015-9733-3. ISBN 978-94-015-9733-3. S2CID 28755980.
↑ Sierra R, Mauffrey F, Cruz J, Holzmann M, Gooday AJ, Maurer-Alcalá X, Thakur R, Greco M, Weiner AKM, Katz LA, Pawlowski J (2022). "Taxon-rich transcriptomics supports higher-level phylogeny and major evolutionary trends in Foraminifera" (PDF). Molecular Phylogenetics and Evolution. 174 (107546): 107546. doi:10.1016/j.ympev.2022.107546. PMID 35690380. S2CID 249608315.
↑ Gooday AJ, Holzmann M, Schwarzgruber E, Cedhagen T, Pawlowski J (2022). "Morphological and molecular diversity of monothalamids (Rhizaria, Foraminifera), including two new species and a new genus, from SW Greenland". European Journal of Protistology. 86: 125932. doi:10.1016/j.ejop.2022.125932. PMID 36347189.
↑ Sergeeva NG, Anikeeva OV (2021). "Vellaria solenta (Monothalamea: Allogromiidae) — new species of soft-walled foraminifera from Sivash Bay (the Sea of Azov)" (PDF). Invertebrate Zoology. 18 (2): 152–158. doi:10.15298/invertzool.18.2.06. S2CID 237368888.
1 2 3 4 5 Siemensma F, Holzmann M, Apothéloz-Perret-Gentil L, Clauß S, Voelcker E, Bettighofer W, et al. (2021). "Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera". European Journal of Protistology. 77: 125744. doi:10.1016/j.ejop.2020.125744. PMID 33191053. S2CID 225144520.
↑ Dellinger M, Labat A, Perrouault L, Grellier P (May 2014). "Haplomyxa saranae gen. nov. et sp. nov., a new naked freshwater foraminifer". Protist. 165 (3): 317–329. doi:10.1016/j.protis.2014.03.007. PMID 24810177.
↑ Maldonado, Manuel; López-Acosta, María; Sitjà, Cèlia; Aguilar, Ricardo; García, Silvia; Vacelet, Jean (10 June 2013). "A giant foraminifer that converges to the feeding strategy of carnivorous sponges: Spiculosiphon oceana sp. nov. (Foraminifera, Astrorhizida)". Zootaxa. 3669 (4). doi:10.11646/zootaxa.3669.4.9. hdl:10261/92975.
↑ Nakamura Y, Tuji A, Kimoto K, Yamaguchi A, Hori RS, Suzuki N (2020). "Ecology, Morphology, Phylogeny and Taxonomic Revision of Giant Radiolarians, Orodaria ord. nov. (Radiolaria; Rhizaria; SAR)". Protist. 172 (3): 125808. doi:10.1016/j.protis.2021.125808. ISSN 1434-4610. PMID 34186475. S2CID 235686052.
↑ Kawachi, Masanobu; Nakayama, Takuro; Kayama, Motoki; Nomura, Mami; Miyashita, Hideaki; Bojo, Othman; Rhodes, Lesley; Sym, Stuart; Pienaar, Richard N.; Probert, Ian; Inouye, Isao; Kamikawa, Ryoma (June 2021). "Rappemonads are haptophyte phytoplankton" (PDF). Current Biology. 31 (11): 2395–2403.e4. doi:10.1016/j.cub.2021.03.012. PMID 33773100. S2CID 232369943.
↑ Hausmann K, Weitere M, Wolf M, Arndt H (2002). "Meteora sporadica gen. nov. et sp. nov. (Protista incertae sedis) – an extraordinary free-living protist from the Mediterranean deep sea". Eur. J. Protistol. 38 (2): 171–177. doi:10.1078/0932-4739-00872.
↑ Shshkin, Yegor (2022). "Spironematella terricola comb. n. and Spironematella goodeyi comb. n. (Hemimastigida = Hemimastigea = Hemimastigophora) for Spironema terricola and Spironema goodeyi with diagnoses of the genus and family Spironematellidae amended". Zootaxa. 5128 (2): 295–297. doi:10.11646/zootaxa.5128.2.8. PMID 36101172.
↑ Heiss AA, Warring SD, Lukacs K, Favate J, Yang A, Gyaltshen Y, Filardi C, Simpson AGB, Kim E (2021). "Description of Imasa heleensis, gen. nov., sp. nov. (Imasidae, fam. nov.), a Deep-Branching Marine Malawimonad and Possible Key Taxon in Understanding Early Eukaryotic Evolution". Journal of Eukaryotic Microbiology. 68 (2): e12837. doi:10.1111/jeu.12837. PMID 33274482. S2CID 227281992.
↑ Stairs CW, Táborský P, Salomaki ED, Kolisko M, Pánek T, Eme L, Hradilová M, Vlček Č, Jerlström-Hultqvist J, Roger AJ, Čepička I (December 2021), "Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes", Current Biology, 31 (24): 5605–5612, doi:10.1016/j.cub.2021.10.010, PMID 34710348
↑ Táborský, Petr; Pánek, Tomáš; Čepička, Ivan (2017). "Anaeramoebidae fam. nov., a Novel Lineage of Anaerobic Amoebae and Amoeboflagellates of Uncertain Phylogenetic Position". Protist. 168 (5): 495–526. doi:10.1016/j.protis.2017.07.005.
↑ Yabuki A, Gyaltshen Y, Heiss AA, Fujikura K, Kim E (2018). "Ophirina amphinema n. gen., n. sp., a New Deeply Branching Discobid with Phylogenetic Affinity to Jakobids". Sci Rep. 8 (1): 16219. Bibcode:2018NatSR...816219Y. doi:10.1038/s41598-018-34504-6. PMC 6212452. PMID 30385814.
↑ Galindo LJ, Prokina K, Torruella G, López-García P, Moreira D (April 2023). "Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch". Genome Biology and Evolution. 15 (4): evad058. doi:10.1093/gbe/evad058. PMC 10139444. PMID 37029959.
↑ Pánek T, Táborský P, Pachiadaki MG, Hroudová M, Vlček Č, Edgcomb VP, Čepička I (2015). "Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage". Frontiers in Microbiology. 6: 1288. doi:10.3389/fmicb.2015.01288. PMC 4649034. PMID 26635756.
↑ Belyaev, Artem O.; Zagumyonnyi, Dmitriy G.; Mylnikov, Alexander P.; Tikhonenkov, Denis V. (2022). "The Morphology, Ultrastructure and Molecular Phylogeny of a New Soil-Dwelling Kinetoplastid Avlakibodo gracilis gen. et sp. nov. (Neobodonida; Kinetoplastea)". Protist. 173 (4): 125885. doi:10.1016/j.protis.2022.125885.
↑ Shishkin, Yegor; Drachko, Daria; Zlatogursky, Vasily V. (22 April 2021). "The smallest known heliozoans are the Erebor lineage (nom. clad. n.) inside Microheliella maris (Eukaryota, Diaphoretickes), with the amendation of M. maris diagnosis and description of Berkeleyaesol magnus gen. nov., comb. nov. (Eukaryota, incertae sedis)". International Journal of Systematic and Evolutionary Microbiology. 71 (4). doi:10.1099/ijsem.0.004776.
↑ Lee, Won Je (2002). "Some free‐living heterotrophic flagellates from marine sediments of inchon and Ganghwa Island, Korea". Korean Journal of Biological Sciences. 6 (2): 125–143. doi:10.1080/12265071.2001.9647643.
↑ Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K (2012). "Prokaryote or eukaryote? A unique microorganism from the deep sea". J Electron Microsc (Tokyo). 61 (6): 423–431. doi:10.1093/jmicro/dfs062. PMID 23024290.

External links

EukMap – Taxonomy Map of the UniEuk Project

This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.

[origin-1] The first eukaryotes were “neither plants, animals, nor fungi”, hence as defined, the Protista would include the earliest common ancestor of all eukaryotes.

[3] In the original 4-kingdom model proposed in 1959, Protista included all unicellular microorganisms such as bacteria.

[Teretosporea_Pluriformea-18] 1 2 3 There are two competing phylogenetic hypotheses: Teretosporea (Corallochytrium + Ichthyosporea) and Pluriformea (Corallochytrium + Syssomonas).^[3] This article follows the latter hypothesis, because it is strongly supported by the most recent phylogenetic studies.^[11]

[Choanozoa-20] The term "Choanozoa" has been used since 1991 by Cavalier-Smith as a paraphyletic assemblage of opisthokont protists, and the terms "Apoikozoa" and "choanimal" were proposed as names for the clade Metazoa+Choanoflagellata. However, these terms have not been formally described or adopted, and were rejected in favour of a renamed Choanozoa to fit the clade Metazoa+Choanoflagellata.^[3]

[Incertae_Corycidia-24] The position of the genera Microcorycia, Parmulina, Penardochlamys and Zonomyxa, which were listed in 2002 under family Microcoryciidae, is not clear. They are placed here by morphological characters but this needs to be supported by molecular data.^[3]

[Variosea-29] The latest revision by Adl et al. (2019) ignores the grouping of some variosean genera into higher rank clades that was made in older studies because of the weakly supported SSU phylogenetic analyses, except for Fractovitellida, which is fully supported by phylogenomic analyses from 2017.^[3]

[nofam-31] 1 2 3 4 5 6 7 This order was initially divided into families, but phylogenetic analyses haven't supported the monophyly of each family. For this reason, in recent classifications there is no family rank division within it.^[19]^[3]

[Mycamoeba-33] This genus groups with Dermamoebidae in a phylogenetic anaysis that uses a limited number of taxa.^[25] In the recent taxonomy it is listed as a separate clade until its position is better resolved.^[3]

[Pessonella-37] This genus could be a synonym of Vannella.^[3]

[Stygamoebida-38] Both genera group together in some phylogenetic analyses, but usually appear separated. They are considered a potential branch of Discosea, unless proven otherwise in the future with better taxon sampling.^[3]

[Microheliella-40] Latest analyses show that Microheliella is the sister group to Cryptista.^[12]

[Telonemia-41] Telonemia is the sister group to the SAR clade.^[9]

[Picozoa-44] The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.^[31]

[Actinophryida-56] Cavalier-Smith and Scoble (2013) show a sister relationship between raphidophytes and Actinophryida.^[42]

[61] Highly divergent 18S rRNA.^[3]

[Stichotrichida-62] This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.^[3]

[Cercozoa-66] 1 2 Initially, Cercozoa contained the clades Filosa and Endomyxa; however it has recently been synonymized with Filosa after a study found Endomyxa more closely related to Retaria.^[48] The current classification places Endomyxa either as the sister clade of Retaria or as part of Retaria, even though more recent studies support the monophyly of Cercozoa as Filosa+Endomyxa again.^[49]

[Tracheleuglypha-70] There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.^[3]

[Heteronematina-96] There is no phylogenetic taxonomy for phagotrophic euglenids. Some possibly monophyletic taxa have been proposed that cover restricted subgroups of the phagotrophic euglenids, such as Ploeotiida (Ploeotia, Entosiphon, Lentomonas, and presumably Keelungia) and Petalomonadida (Petalomonas, Notosolenus and Calycimonas, and presumably also taxa such as Sphenomonas). There is a limited taxon sampling for molecular data, and many traditional genera are probably paraphyletic.^[3]

[Coelosporidium-99] Probably a synonym of the zygomycete fungus Nephridiophaga.^[3]

[Luffisphaera-101] May be the same genus as Belonocystis.^[3]

[103] It is not yet known whether this organism is an eukaryote or a prokaryote.^[81]

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[Broad_monothalamids-83] 1 2 3 4 5 Siemensma F, Holzmann M, Apothéloz-Perret-Gentil L, Clauß S, Voelcker E, Bettighofer W, et al. (2021). "Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera". European Journal of Protistology. 77: 125744. doi:10.1016/j.ejop.2020.125744. PMID 33191053. S2CID 225144520.

[Haplomyxa_saranae-84] Dellinger M, Labat A, Perrouault L, Grellier P (May 2014). "Haplomyxa saranae gen. nov. et sp. nov., a new naked freshwater foraminifer". Protist. 165 (3): 317–329. doi:10.1016/j.protis.2014.03.007. PMID 24810177.

[Spiculosiphon_oceana-85] Maldonado, Manuel; López-Acosta, María; Sitjà, Cèlia; Aguilar, Ricardo; García, Silvia; Vacelet, Jean (10 June 2013). "A giant foraminifer that converges to the feeding strategy of carnivorous sponges: Spiculosiphon oceana sp. nov. (Foraminifera, Astrorhizida)". Zootaxa. 3669 (4). doi:10.11646/zootaxa.3669.4.9. hdl:10261/92975.

[Orodaria-86] Nakamura Y, Tuji A, Kimoto K, Yamaguchi A, Hori RS, Suzuki N (2020). "Ecology, Morphology, Phylogeny and Taxonomic Revision of Giant Radiolarians, Orodaria ord. nov. (Radiolaria; Rhizaria; SAR)". Protist. 172 (3): 125808. doi:10.1016/j.protis.2021.125808. ISSN 1434-4610. PMID 34186475. S2CID 235686052.

[Rappephyceae-87] Kawachi, Masanobu; Nakayama, Takuro; Kayama, Motoki; Nomura, Mami; Miyashita, Hideaki; Bojo, Othman; Rhodes, Lesley; Sym, Stuart; Pienaar, Richard N.; Probert, Ian; Inouye, Isao; Kamikawa, Ryoma (June 2021). "Rappemonads are haptophyte phytoplankton" (PDF). Current Biology. 31 (11): 2395–2403.e4. doi:10.1016/j.cub.2021.03.012. PMID 33773100. S2CID 232369943.

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[Spironematellidae-89] Shshkin, Yegor (2022). "Spironematella terricola comb. n. and Spironematella goodeyi comb. n. (Hemimastigida = Hemimastigea = Hemimastigophora) for Spironema terricola and Spironema goodeyi with diagnoses of the genus and family Spironematellidae amended". Zootaxa. 5128 (2): 295–297. doi:10.11646/zootaxa.5128.2.8. PMID 36101172.

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Current classification

Amorphea Adl et al. 2012

Obazoa Brown et al. 2013

Opisthokonta Cavalier-Smith 1987, emend. Adl et al. 2005

Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998

Tubulinea Smirnov et al. 2005

Evosea Kang et al. 2017

Discosea Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011

Diaphoretickes Adl et al. 2012

Archaeplastida Adl et al. 2005

SAR Burki et al. 2008, emend. Adl et al. 2012

Stramenopiles Patterson 1989, emend. Adl et al. 2005

Alveolata Cavalier-Smith 1991

Rhizaria Cavalier-Smith 2002

Haptista Cavalier-Smith 2003

Cryptista Cavalier-Smith 1989, 2018, emend. Adl et al. 2019

Incertae sedis Eukarya

Hemimastigophora Foissner et al. 1988

Excavates (P)

Malawimonadida Cavalier-Smith 2003

Metamonada Grassé 1952, emend. Cavalier-Smith 1987

Discoba Simpson in Hampl et al. 2009

Clades basal to Amorphea

Genera of uncertain affiliation

See also

Notes

References

External links