The mission founded in 1817 in San Rafael had fallen to disrepair by the 1860s, and was completely demolished in 1870. Sixty-five years later, the Marin County Historical Society (MCHS) was formed, and within months of its establishment, the society began a search to recover and preserve the old mission bells. At a society meeting in August, 1935, there was discussion of one bell located at the home of Mrs. James Burdell of Olompali, and possible locations of a second and third bell. In June of 1943, Mrs. Burdell donated the first mission bell to the Marin County Historical Society.
By 1943, plans were already proposed to recreate the old mission beside the Church of Saint Raphael, which had been built in 1919. Then City Mayor William S. Nock worked with officers of the MCHS on the project, and three members of the society, President George H. Harlan, IJ reporter Florence Donnelly, and Mayor Nock, were appointed by the City Council to do the groundwork for the restoration. In January, 1947, it was announced that the newspaper publisher William R. Hearst was contributing $500,000 for the restoration of the California missions, and according to the Marin Independent-Journal of December 19, 1949, the MCHS committee submitted all of the dimensions, descriptions, and location details to the administrators of the fund. After conferring with Archbishop John J. Mitty of the SF Archdiocese, and the hiring of church architect Arnold Constable of Sausalito, the plans were approved and $85,000 was allocated for the construction of the replica.
On May 22, 1949, during San Rafael’s Fiesta Days weekend, construction began, and on December 18, 1949, Archbishop Mitty presided over the dedication of the newly constructed Mission San Rafael Arcángel. On May 19, 1950, MCHS had the first public viewing of exhibits of society artifacts in the historical room of the Mission. Two of the recovered mission bells were hung at the entrance to the new replica, and efforts were under way to recover one of the pear trees from the once-flourishing mission orchard. In 1959, the MCHS collections and exhibits were moved to the Boyd Gate House, the current exhibit space for the renamed Marin History Museum.