It was the only mission built in Alta California after Mexico gained independence from Spain. The difficulty of its beginning demonstrates the confusion resulting from that change in governance.
The California Governor wanted a robust Mexican presence north of the San Francisco Bay to keep the Russians who had established Fort Ross on the Pacific coast from moving further inland. A young Franciscan friar from Mission San Francisco de Asis wanted to move to a location with a better climate and access to a larger number of potential converts.
The Mission was successful, given its short eleven year life, but was smaller in number of converts and with lower productivity and diversity of industries than the older California missions. The mission was not thriving because of its climate and had established a medical asistencia "sub-mission" in San Rafael to help the mission's ill neophytes baptized Native Americans recover their health.
The legislature approved but the church authorities did not respond they had forwarded the plan to their superiors in Mexico. Beginning in , while waiting for a response from the church authorities, Fr.
Altimira, with military escorts, began exploring north of the Bay for a suitable mission site. On July 4, , the soldiers placed a large redwood cross on the place in the Sonoma Valley where they expected the new Mission San Francisco de Assis to be established.
