It was originally intended to be an _asistencia_ of San Francisco, but although there is no record that it was ever formally raised to the dignity of an independent Mission, it is called and enumerated as such from the year 1823 in all the reports of the Fathers.

To-day, not a brick of its walls remains; the only evidence of its existence being the few old pear trees planted early in its history.
There are those who contend that San Rafael was founded as a direct check to the southward aggressions of the Russians, who in 1812 had established Fort Ross, but sixty-five miles north of San Francisco.
There seems, however, to be no recorded authority for this belief, although it may easily be understood how anxious this close proximity of the Russians made the Spanish authorities.
They had further causes of anxiety.

The complications between Mexico and Spain, which culminated in the independence of the former, and then the establishment of the Empire, gave the leaders enough to occupy their minds.
The final establishment took place in 1823, without any idea of founding a new Mission.

The change to San Rafael had been so beneficial to the sick Indians that Canon Fernandez, Prefect Payeras, and Governor Argueello decided to transfer bodily the Mission of San Francisco from the peninsula to the mainland north of the bay, and make San Rafael dependent upon it.

An exploring expedition was sent out which somewhat carefully examined the whole neighborhood and finally reported in favor of the Sonoma Valley.