Mission Santo Tomás de Aquino was founded in what is now Baja California on April 24, 1791 by the Dominican missionary José Loriente, with the authorization of the president of the missions, Juan Crisóstomo Gómez. It was named for Saint Thomas Aquinas.
The mission was established in the territory of the Kumeyaay, on the mountainside of the San Solano hills in northwestern Baja California, Mexico. It bridged the 120-kilometer gap between the previously founded missions of San Vicente and San Miguel.
The mission was relocated twice, in around 1794 and in 1799. Historians are uncertain concerning the locations of the first two mission sites. The third and final location was at the modern town of Santo Tomás.
The population was over 250 individuals in 1800, and it reached its peak of 400 in 1824. The mission was secularized in 1833, but a priest continued to serve the neophytes until 1849. In that year, the native population had fallen to 60, and the mission was abandoned to the military, who used it as a fort and capital for northern Baja California. Deteriorating ruins survive at the site.
The mission was built in a large valley crossed by two or three little springs in the town that today bears the name of the former mission.
Among the flora that the missionaries found were mezcal, chamizo, alder, willow, oak, poplar, and elderberry.
Agricultural crops included wheat, olives, grapes, maize, barley, beans, and other vegetables, all of which were cultivated using irrigation. It is estimated that the mission had around 80-178 hectares of farm land.