Especially after the American conquest of California in 1846-1848, the surviving Muwekma people sought refuge on six rancherias located within their ancestral homelands on the eastern side of San Francisco Bay.

During the mid-19th century, as the rest of the central California Indians were displaced and at times hunted down, Alisal (located near Pleasanton, California) as well as the other rancherias became safe-havens for the Muwekma Ohlone Indians and members from the interior tribes who had intermarried with them at the missions.