It was originally the site of the Misión Santo Tomás de Aquino. After the mission was abandoned, it was taken as a post for the Mexican frontier garrison and for a time as the capital of the territory of Baja California. The town grew up east of the Mission site.
Economy
Santo Tomás is a wine-growing region, home to numerous vineyards and wineries. Since the rise in popularity of Valle de Guadalupe as a premier wine region in Baja California, Santo Tomás has begun to develop tourist accommodations, such as hotels and fine dining.