The San Joaquin kit fox (Vulpes macrotis mutica) is endemic to central California, and is listed as Federally Endangered and California Threatened, primarily due to profound habitat loss. This loss continues and habitat protection is urgently needed for the conservation and eventual recovery of the kit fox. To identify lands to target for habitat protection, we used a GIS-based map-algebra model to determine the distribution of remaining suitable habitat for San Joaquin kit foxes. The primary variables used in the model included land use/land cover, vegetation density, and terrain ruggedness. Suitability was categorized as high, medium, or low based on habitat attributes relative to the presence and persistence of kit fox populations. Model results indicated that only 4,140 km2 of high suitability habitat and 7,268 km2 of medium suitability habitat remain for San Joaquin kit foxes, and much of this habitat is highly fragmented. High suitability habitat primarily is concentrated in the southern portion of the kit fox range with some also scattered along the western edge of the San Joaquin Valley. Persistent kit fox populations appear to occur only in areas with relatively large patches of high suitability habitat or a mix of high and medium suitability habitat. Kit fox populations are apparently unable to persist in areas with high habitat fragmentation or areas with primarily medium suitability habitat. Our results underscore the urgent need to focus protection efforts on high suitability habitat and to do so in a manner that increases patch size of protected lands.