The mission is located in the San Miguel Valley. 

This site was known as San Juan Bautista, and during the journey to Alta California, Father Juan Crespi recognized it as an ideal place to establish a mission, which was founded on March 12, 1787, by the Dominican Luis de Sales. 

The following year, it moved its original settlement seven kilometers upstream. 

In 1834, it was abandoned due to a lack of personnel. It was the fourth mission located on the Camino Real. 

Currently, isolated adobe walls of the Dominican Mission remain.