The first church in Iloilo was built by the Jesuits around 1607 to serve the needs of the military stationed in Punta, as Iloilo was then called. However, on 29 April 1617, the Augustinians established San José, a house of the order. They held San José until 1775 when administration was given to the secular clergy. In 1868, Iloilo along with La Paz (Loboc) was given to the Augustinians in exchange for Jaro which had become the seat of the newly founded diocese. Fr. Mauricio Blanco was named prior in 1873 and he started enlarging and repairing an older church built of light material. Later he decided to build a new church of stone and brick, after the Miguelete church of Valencia del Cid (Spain). However, he was unable to fulfill his plans, and stopped when he had completed two stories. He finished the church, added two towers one with a clock and barometer and built a convent. The towers were begun on 14 November 1893. The church was repaired in 1902 under Fr. Manuel Diez, restored in 1945 under architect and engineer Mariano Cacho following plans by Fr. David Caseres. The altars were gilded by Fr. Jesús Fernandez. During World War II, the church was saved from being bombed by the Americans after they received information that Japanese were not holed in the church as they were previously informed. Between 1980-82 the church was renovated, a new marble floor was laid, under the direction of poet-writer, Fr. Gilbert Centina. San José is one of the few parish in the Philippines still under the Augustinians.
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