Mission San Rafael Arcángel was one of the first missions turned over to the Mexican government in 1833. In 1840, there were 150 Indians still at the mission. By 1844, Mission San Rafael Arcángel was left abandoned. What was left of the empty buildings was sold for $8,000 in 1846. The mission was used by John C. Fremont as his headquarters during the battles to make California a United States possession. In 1847, a priest was once again living at the mission. A new parish church was built near the old chapel ruins in 1861. In 1870, the rest of the ruins were removed to make room for the city of San Rafael. All that was left of the mission was a single pear tree from the old mission's orchard. In 1949, Monsignor Thomas Kennedy rebuilt and restored the chapel.
Today the Mission San Rafael Arcángel sits next to the parish church of St. Raphael. It is located on the site of the original hospital. It is open to visitors and has a small museum and gift shop.
See also: California mission