During the 2006 and 2007 breeding seasons, we conducted a systematic survey for western burrowing owls (Athene cunicularia hypugaea) across the portions of California's southeastern deserts that had never been systematically surveyed for the species. We found few or no western burrowing owls in northern and eastern portions of the Mojave Desert or in the Sonoran Desert (excluding Palo Verde Valley). However, there was a substantial concentration of burrowing owls in the western Mojave Desert, which we estimated to contain ≤560 (SE  =  268) breeding pairs. We also documented 179 breeding pairs along the banks of water-conveyance structures in Palo Verde Valley in the Sonoran Desert region. These two disjunct populations comprise a significant portion of the population of burrowing owls in California.