The next to the last Franciscan mission established in California; founded as an asistencia or branch of San Francisco (Dolores). The mortality among the Indians in San Francisco had become so great that a panic was feared, and a transfer of a portion of the survivors to some situation on the north side of the bay was proposed. At first they were sent over without a priest, but after several had died it was determined to found a new establishment; this was done, Dec. 14, 1817, the new mission being dedicated to San Rafael Arcángel.
The native name of the place was Nanaguami. About 230 neophytes were transferred from San Francisco, most of whom, however, originally came from the north side of the bay. An adobe building, 87 by 42 ft, divided into rooms for chapel, dwelling rooms, etc., was finished in 1818. Two years later there were 590 neophytes, and 1,140, the highest number reached, in 1828. By 1823 the establishment was recognized as a separate mission. Its wealth was never very great, though it was prosperous, having in 1830, 1,548 large stock and 1,852 sheep, with an average crop for the preceding decade of 2,454 bushels. In 1830 there were 970 neophytes, the number decreasing about 50 percent in the next four years. At the time of secularization considerable property was distributed among the Indians; but in 1837, under the plea that the natives were not making good use of it, this was again brought together, with a promise of redistribution under more favorable circumstances. In 1839 the Indians were reported to be greatly dissatisfied, and in 1840 a distribution of the livestock was ordered.
There were then 190 Indians near the mission, and probably 150 more scattered elsewhere. In 1846 Fremont took possession of the mission. After he left, it seems to have been unoccupied, and it has now entirely disappeared.
The neophytes probably belonged chiefly to the Olamentke division of the Moquelumnan family.