For many years Mission San Rafael was all but forgotten. San Raphael’s Church, preserving at least the name of the mission 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.
Originally Mission San Rafael was an 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 had suffered from white man’s diseases, aggravated by the damp and foggy climate. It was 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 Sarria on December 14, 1817, and named for Saint Raphael, the angel of bodily healing.
At the end of a year the asistencia population stood at 300, mostly Indians transferred from 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 became a full-fledged and independent mission. Livestock and agricultural production increased. The mission pears soon were greatly desired in the area.
San Rafael was the first mission to be secularized. General Mariano Guadalupe Vallejo, the commandante of the San Francisco presidio, who owned great estates in the north Bay Area, logically turned up as the first administrator. All of the mission livestock was transferred to the great Vallejo 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 Mission Indians to destroy their own mission!