Father Nicolas Tamaral established the Mission San Jose del Cabo Anuiti in 1730 as part of the Jesuit colonization of the peninsula of Baja California. The building site was moved by the missionaries on several occasions in an attempt to flee from epidemics and mosquito infestations, while securing a source of fresh water. Early buildings were simple structures of adobe, sticks and palm fronds, vulnerable to storm damage.
In 1734, the region’s Pericu Indians destroyed the four southern missions, including the Mission of San Jose. Father Tamaral was murdered with great cruelty during the uprising which is depicted on the tile mural above the church’s entrance.
The Jesuits left the Baja Peninsula in 1768, to be followed by the Franciscans and then the Dominicans. The Combonian missionaries served the Mission of San Jose from 1948 to 1986. Since, the church has been in the hands of diocesan clergy.
The twin-towered church seen today was built in 1932, at the traditional location on the plaza long occupied by the Mission of San Jose.