By the early 1700's, the Spanish Franciscans had established a network of 40 missions in Northern and Central Florida, with 70 priests ministering to over 25,000 Native American converts.

[2] However, raids by British settlers and their Creek Native American allies from the Carolinas eventually shut down the missions.

Part of the reason for the raids was that the Spanish colonists gave refuge to enslaved people who had escaped the Carolinas.

After the end of the French and Indian War in 1763, Spain ceded all of Florida to Great Britain for the return of Cuba.

Given the antagonism of Protestant Great Britain to Catholicism, the majority of the Catholic population in Florida fled to Cuba.

[8] In 1850, Pope Pius IX erected the Diocese of Savannah, which included Georgia and all of Florida east of the Apalachicola River.

[11] During the American Civil War, Vérot condemned the looting of the Catholic church at Amelia Island, Florida, by Union Army troops.

[12] After the war, Vérot published a pastoral letter urging Catholics in the diocese to "put away all prejudice ... against their former servants".

In 1866, the Sisters of St. Joseph were introduced from France, and despite the most adverse conditions, they had several flourishing schools and academies in operation before many years.

On March 11, 1870, Pius IX elevated the Vicariate of Florida into the Diocese of St. Augustine and named Vérot as its first bishop.

At Moore's request, a group of Jesuit fathers arrived in Tampa, Florida, in 1888 to replace the priests lost to illness.

With the local priest William J. Kenny sidelined by the disease, Moore rushed there to run the parish and tend to the sick.

[15] In 1913, the Florida Legislature had passed legislation prohibiting white women from teaching African-American children, a measure aimed at non-segregated Catholic schools.

In 1916, Florida Governor Park Trammell ordered the arrest of three Sisters of St. Joseph for violating the law on teaching African-American children.

[16][17] Curley attracted national attention in 1917 by successfully battling a bill in the Florida Legislature that would have mandated inspections of convents.

[23] Hurley was a staunch opponent of the American Civil Rights actions during the 1960s, even avoiding Martin Luther King Jr. at the airport when their paths crossed unexpectedly.

Galeone retired in 2011 and Pope Benedict XVI replaced him with Auxiliary Bishop Felipe de Jesús Estévez of Miami.

He attended the installation of Bishop Robert Schaefer of the Evangelical Lutheran Church in America near Tampa, Florida.

He collaborated with local Eastern Orthodox Christian leaders in support of the meeting between Pope Francis and Patriarch Bartholomew in Jerusalem in 2014.

In March 2020, the diocese removed Reverend John H. Dux from ministry after determining that sex abuse allegations against him from 1976 were credible.