From 1607 to 1910 the entire island of Mindanao was under the Diocese of Cebu and Jaro.  On April 10, 1910, Pope Pius X created the Diocese of Zamboanga and gave it jurisdiction over the whole island of Mindanao, including the adjacent islands of the Sulu Archipelago and the island of Cagayan de Sulu.

The faith first came to Zamboanga in 1635 with the arrival of the first missionaries, Father Melchor de Vera and Father Alejandro Lopez, both Jesuits.  The Spanish authorities were always at war with the Muslims then.  Their efforts to subdue the Muslims always resulted in reprisal raids in Zamboanga and the Visayan Islands.  In Zamboanga, Fort Pilar, in honor of Our Lady of the Pillar, was constructed in 1636.  Two Jesuits priests died as martyrs in their efforts to win the Muslims through diplomacy – Father Francisco Paliola and Father Alejanrdo Lopez.

On January 20, 1933, Pope Pius XI divided the Mindanao area into two – the whole southern portion, including the Sulu Archipelago, under the jurisdiction of Zamboanga, and the northern portion under the Diocese of Cagayan de Oro.  In 1951, Cagayan de Oro was elevated to an archdiocese, the first in the island of Mindanao.  And all episcopal jurisdictions in Mindanao and Sulu, including that of Zamboanga, became suffragans of this archdiocese.

The Diocese of Zamboanga was further divided when the Diocese of Davao was established and separated in 1949; the Prelature of Cotabato in 1950; the Prelature of Isabela, Basilan, in 1967, and finally the Prelature of Ipil in 1980.

Zamboanga was raised to an archdiocese on May 15, 1958 by Pope Pius XII.  As an ecclesiastical province, the Archdiocese of Zamboanga now comprises the City of Zamboanga and part of the province of Zamboanga del Sur.  As suffragans it has the Prelature of Ipil, also in Zamboanga del Sur, the Prelature of Isabela, Basilan, and the Apostolic Vicariate of Jolo.  Its titular patroneses is Our Lady of the Pillar, and its secondary patron is St. Pius X, Pope.

The archdiocese today covers a land area of 1,648 square kilometers and a population of 442,345 of which 81 per cent are Catholics.  The area covers 20 parishes, served by 49 diocesan and 18 religious priests.  There are also 51 religious sisters working in related activities in the archdiocese.

The Second Plenary Council of the Philippines adopted the Community of Disciples as the prime model of the Church, with the special attribute of being a Church of the Poor.  For the church in Zamboanga, the challenge is to incarnate in the archdiocese the vision of PCP II.

An Archdiocesan Pastoral Assembly was held early in 1995 to formalize preparations leading to Second Archdiocesan Pastoral Assembly of Zamboanga in 1996.

Among the Catholic institutions in the Archdiocese of Zamboanga are 2 colleges, 6 secondary schools, 6 elementary schools, and 8 kindergarten schools.  Charitable and social institutions include a leprosarium, 5 free clinics, 1 orphanage and 1 child center.