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Mission San Rafael Arcangel, was founded on December 14, 1817 by Father Vicente de Sarria. It was the 20th mission in the 21 mission chain in Alta California. It was named for Saint Raphael, the angel of healing. The mission was established as a hospital to treat the sick Indians from Mission San Francisco de Asis. The San Rafael warm weather helped heal the sick and injured Indians. On October 19, 1822, San Rafael was declared independent of Mission Dolores and raised to full mission stature.

The Indians patients had a difficult beginning at the mission. Many Indians were healed and cured under the care of Father Luis Gil who ran the hospital. Father Juan Amoros taught the Indians the trades. They became expert boatbuilders, blacksmiths, cowboys, carpenters and weavers. Many of the local Miwok Indians came to live at the mission. By 1828, there were 1,140 Indians living at the mission.