Mission San Miguel was established on 28 March 1787 by the Dominican missionary Luis Sales among the Kumeyaay Indians of northwestern Baja California, Mexico. The ruins of the mission are located in present-day Ejido La Misión, Baja California in the municipio of Ensenada. The mission ruins are behind the local school, on the north side of Highway 1.
It was near this place that, in 1773, a large cross was erected to indicate the boundary of missionary responsibilities in Las Californias between Franciscans (north) and Dominicans (south). Franciscan missionary Francisco Palóu, on his way to San Diego, supervised the operation. In 1804, the same line was used to divide Las Californias into separate provinces of Alta California and Baja California. Today's border between the United States and Mexico is about 30 miles (48 km) to the north.
The mission was built with the support of six soldiers from the Presidio of San Diego and five others probably from Mission San Vicente. They had just begun to build the first houses and plant the first crops when the neighboring San Juan Bautista Creek ran dry. This forced them to move the mission to a new site called San Juan Bautista, 10 km upstream, where there was a good supply of water.
The enclosure was rectangular, with the church and the residential quarters facing east and south. It had an open patio, the only entrance to which was a large door located in the southeast corner of the complex, protected by a barrack. The complex also included an irrigation ditch, four granaries, two houses, a corral, and three other rooms.
The buildings of the complex were made of adobe, with round stone foundations, set at a depth of 90 cm, cemented with a mortar of clay, sand, and lime. The adobe bricks resting on the foundation were cemented with the same mortar and placed in an alternating fashion to give the structure more strength and stability, making walls from 0.9 to 1.1 m thick. The adobe was made with local soil, water, clay, sand, and straw to make it more resistant.