For many years, Mission San Rafael was all but forgotten. San Raphael’s Church, preserving at least its name in English, stood on the approximate site. Finally, a chapel, built to resemble existing pictures of the old mission church, was crowded onto Saint Raphael’s property.
Initially, Mission San Rafael Arcángel was a medical Asistencia or outpost chapel of the San Francisco mission. Also, it was known as the first Sanitarium in California. For many years, the Indians at Dolores Mission had suffered from white man’s diseases, aggravated by the damp and foggy climate. The Mission Fathers thought the sunny hillside north of the Golden Gate would be a far more healthful location. Thus, the Sanitarium was founded by Father Vicente de Sarría on December 14, 1817, and named for Saint Raphael, the angel of bodily healing.
At the end of the year, the Asistencia population stood at 300, mostly American Indians transferred from Mission Dolores but including a handful of converts from the vicinity. In five years, there was a healthy settlement of over 1,000 neophytes, so on October 19, 1822, San Rafael Arcángel became a full-fledged and independent mission. Livestock and agricultural production increased. The mission pears soon were greatly desired goods in the area.
San Rafael Arcángel was the first mission secularized. General Mariano Guadalupe Vallejo, the Commandant of the San Francisco Presidio, who owned great estates in the north Bay Area, became the first Secular Administrator. Vallejo transferred all mission livestock to his vast ranchos, along with movable equipment and supplies. Even the vines and pear trees were dug up and replanted on the General’s property. He hired the poor Indian converts to destroy the mission that once was theirs!