Mission Santa Rosalía de Mulegé was founded in 1705 by the Jesuit missionary Juan Manuel. The site lies near the entrance of Bahía de Concepción, on the Gulf of California coast.

Construction of a stone church was begun in 1766. In 1768,the Franciscans took over responsibility for Baja California from the Jesuits. By 1770 the mission was virtually deserted. The Dominicans, who succeeded the Franciscans in 1773, began rebuilding, but the population remained less than 100. The mission ceased to function in 1828. The present church buildings have been extensively restored.