1700 to 1840

The first Roman Catholic churches in the current territory of the Diocese of San Diego were two of the twenty-one "California Missions" (Mission San Diego de Alcala and Mission San Luis Rey de Francia).

During the 18th century, the San Bernardino and Riverside areas were part of the province of Las Californias in the Spanish colony of New Spain.

• The Mission San Diego de Alcalá was founded in 1769 by Reverend Junipero Serra in present day San Diego.^[3]
• The Mission San Luis Rey de Francia was established in present day Oceanside by Reverend Fermín de Lasuén in 1798.^[4]

In 1804, the Spanish split the Province of California into two territories:

• Alta California (Upper California), including the modern American states of California, Nevada, Arizona, and Utah, along with western Colorado and southwestern Wyoming
• Baja California Territory (Lower California), including the modern Mexican states of Baja California and Baja California Sur

After the Mexican War of Independence ended in 1821, Alta California became part of Mexico. The Mexican Government in 1835 secularized all the Catholic missions in Alta California, including the Mission San Luis Rey and Mission San Diego.

1840 to 1936

In 1840, Pope Gregory XVI set up the Diocese of California.^[5] The new diocese included both Alta California and Baja California. Gregory XVI set the episcopal see at San Diego in Alta California. The first bishop of the new diocese was Francisco Garcia Diego y Moreno. Moreno designated the Mission Santa Barbara in Santa Barbara as his pro-cathedral.

After ceding Alta California to the United States at the close of the Mexican–American War in 1848, the government of Mexico objected to San Diego, a see city now located in the United States, having jurisdiction over Mexican parishes. In response, the Vatican divided the Diocese of California into American and Mexican sections in 1849. The American section became the Diocese of Monterey; the see city was moved to Monterey because of its more central location. The Royal Presidio Chapel in Monterey became the cathedral of the new American diocese.^[5]

In 1859, Pius IX renamed the Diocese of Monterey as the Diocese of Monterey-Los Angeles to recognize the growth of Los Angeles; the see was transferred to Los Angeles in 1876.^[5] In 1922, the Vatican divided the Diocese of Monterey-Los Angeles, , with the southern portion becoming the Diocese of Los Angeles-San Diego.^[6]

1936 to 1969

The Diocese of San Diego was erected on July 11, 1936, by Pope Pius X, taking San Diego, Imperial, Riverside, and San Bernardino Counties from the new Archdiocese of Los Angeles.^[6] The pope named Reverend Charles F. Buddy from the Diocese of Saint Joseph as the first bishop of San Diego.

Buddy was close friends with Auxiliary Bishop William O'Brien, director of the Catholic Church Extension Society of Chicago. The Society donated money to the new diocese for the construction of churches and the financial support of priests.^[7] Buddy co-founded the University of San Diego in 1949, serving as its first president from 1950 to 1966.^[8]Pope Paul VI appointed Auxiliary Bishop Francis Furey from the Archdiocese of Philadelphia as coadjutor bishop of San Diego in 1963 to assist Buddy.^[9]

After Buddy died in 1966, Furey automatically succeed him as bishop of San Diego. Three years later, in 1969, Furey became archbishop of the Archdiocese of San Antonio.^[9] To replace Furey in San Diego, Paul VI that same year appointed Bishop Leo Maher from the Diocese of Santa Rosa.^[10]

1969 to 1990

At the time of Maher's arrival, the diocese was about $15 million in debt, which Maher fully retired by 1980.^[11] He presided over the second diocesan synod from 1973 to 1976, revising the statutes and guidelines of the diocese to implement the reforms of the Second Vatican Council.^[12] In 1976, Maher created the first Diocesan Pastoral Council.^[12] He ended the official relationship between the diocese and the University of San Diego, establishing the school as a separate corporation.^[11]

Maher was a strong supporter of the ecumenical movement, co-founding the San Diego County Ecumenical Conference and issuing joint statements on morality with non-Catholic religious leaders.^[13] He also supported workers' rights to organize into unions, but pledged an official neutrality in a farm labor dispute in 1971.^[14] That same year, he suspended Reverend Victor Salandini, a San Diego priest and ally of labor organizer César Chávez, for wearing a serape with the black eagle symbol of the United Farm Workers instead of proper vestments and for using corn tortillas instead of sacramental bread during his masses.^[14] In 1975, Maher prohibited Catholics who are members of pro-choice organizations from receiving communion or serving as lectors, specifically citing the National Organization for Women for its "shameless agitation."^[15]

In 1978, Pope John Paul II erected the Diocese of San Bernardino, removing Riverside and San Bernardino Counties from the Diocese of San Diego.^[6]

In 1980, Maher issued a public condemnation of the Ku Klux Klan, saying that knowingly voting for a racist or a Klan member may constitute a sin.^[16] He prohibited priests from celebrating Mass for Dignity, a pro-LGBTQ+ Catholic organization, but once celebrated a mass himself for HIV/AIDS patients at St. Joseph's Cathedral.^[16] In 1989, John Paul II appointed Bishop Robert Brom from the Diocese of Duluth as coadjutor bishop to assist Maher.^[17]

1990 to present

After Maher retired in 1990, Brom automatically succeeded him as bishop of San Diego. Brom was responsible for the creation of two Catholic high schools:

• Mater Dei Catholic High School in Chula Vista, replacing Marian Catholic High School in Imperial Beach
• Cathedral Catholic High School in Carmel Valley, replacing University of San Diego High School in Linda Vista

Brom also created a pastoral center in San Diego after selling the former chancery building to the University of San Diego. In 2012, Pope Benedict XVI named Auxiliary Bishop Cirilo Flores from the Diocese of Orange as coadjutor bishop in San Diego. When Brom retired in 2013, Flores became the next bishop of San Diego.^[18] However, Flores died from a stroke and cancer in September 2014.^[19]

In March 2015, Pope Francis appointed Auxiliary Bishop Robert McElroy from the Archdiocese of San Francisco as bishop of San Diego.^[20] The pope named McElroy cardinal in May 2022.^[21]

Clergy sexual abuse cases

A 16 year old boy in 1977 filed a complaint of sexual assault against Reverend John Daly with the Holtville police. The boy said that Daly picked up him and a companion while hitchhiking and offered to let them stay for the night at St. Joseph Church. The boy awoke in the middle of the night to find Daly performing oral sex on him. Three days after Daly's arrest, the local district attorney told police that the diocese would send Daly away for treatment and that it was dropping charges. In 2002, the 1977 complainant sued the diocese.^[22]

Reverend Edward Rodrigue pleaded no contest in 1979 of sexually abusing an 11 year old developmentally disabled boy in Highland. The diocese removed him from ministry and sent him for 11 months of treatment at a center in Azusa. He was laicized in 1992.^[23] After being arrested in 1997 for child abuse, Rodrigue admitted to sexually abusing dozens of children during his time as a priest. Rodrigue was sentenced to 10 years in prison for abusing children in 1998. By the end of 2004, 15 men had sued the diocese, claiming they were sexually abused by Rodrigue.^[24]

Five women sued the diocese in 2003, claiming that they had been sexually assaulted as minors by Reverend Franz Robier during the 1950s. The victims included four orphans from Europe living at a facility in the diocese. Records showed that Bishop Buddy sent Robier away for treatment after receiving complaints, then allowed him later to resume ministry.^[25][26]

In February 2007, the diocese filed for bankruptcy protection after the diocese was unable to reach a settlement agreement with numerous plaintiffs suing over sexual abuse by clergy.^[27] In September 2007, the diocese agreed to pay $198.1 million to settle 144 claims of child sexual abuse by clergy, the 2nd-largest settlement payment by a Roman Catholic diocese in U.S. history.^[28] Perpetrators included 48 priests and one lay coordinator of altar boys.^[29] In September 2018, the diocese added eight more priests to its list of clergy with credible accusations of abuse.^[30]

In December 2018, Reverend Juan Garcia Castillo from St. Patrick Parish in Carlsbad was convicted of sexual battery. An adult seminarian had accused Castillo of sexually assaulting him while dining at a restaurant with another seminarian. When the accuser was in the mens room, Castillo grabbed his genitals.^[31][32] Castillo was sentenced to 60 years in jail and three years of probation.^[33]

On December 11, 2019, it was announced that four victims of convicted, and now deceased, sexual abuser Anthony Edward Rodrigue would sue the Diocese of San Diego.^[34][35] Their lawsuit began on January 2, 2020, along with 5 lawsuits targeting 5 other priests accused of child molestation and rape.^[34][36][35] Due to all these more recent allegations, the Diocese of San Diego and five other California dioceses established in 2019 a fund for clergy sex-abuse victims; by September 2021 this compensation program had already paid another $24 million in claims.^[37]

Bishops of San Diego

1. Charles Francis Buddy (1936–1966)
2. Francis James Furey (1966–1969, coadjutor bishop 1963–1966), appointed Archbishop of San Antonio
3. Leo Thomas Maher (1969–1990)
4. Robert Henry Brom (1990–2013, coadjutor bishop 1989–1990)
5. Cirilo Flores (2013–2014, coadjutor bishop 2012–2013)
6. Cardinal Robert W. McElroy (2015–present)

Auxiliary bishops

• Richard Henry Ackerman, C.S.Sp. (1956–1960), appointed Bishop of Covington
• John R. Quinn (1967–1971), appointed Bishop of Oklahoma City-Tulsa and later Archbishop of Oklahoma City and Archbishop of San Francisco
• Gilbert Espinosa Chávez (1974–2007)
• Salvatore J. Cordileone (2002–2009), appointed Bishop of Oakland and later Archbishop of San Francisco
• John P. Dolan (2017–2022) appointed Bishop of Phoenix
• Ramon Bejarano (2020–present)
• Michael Phạm Minh Cường (2023-present)
• Felipe Pulido (2023-present)

Other priest of this diocese who became bishop

Phillip Francis Straling, appointed Bishop of San Bernardino in 1978

High schools

• Academy of Our Lady of Peace – Normal Heights, San Diego. It is administered by the Sisters of St. Joseph of Carondelet.
• Cathedral Catholic High School – Carmel Valley, San Diego. It was formerly the University of San Diego High School.
• Mater Dei Catholic High School – Chula Vista. It was formerly Marian Catholic High School.
• St. Augustine High School – North Park, San Diego. It is administered by the Augustinians.
• Vincent Memorial Catholic High School – Calexico