Although the San Joaquin kit fox (Vulpes macrotis mutica) has been a federally protected subspecies since 1967, current information on its status throughout much of its historical range is lacking. Since 1983, only 5 surveys have been conducted, and a recent recovery plan emphasized the need for better information on the status of this subspecies. Between 2001 and 2003, we attempted to obtain new information on this kit fox on specific public and private properties in 8 counties in the San Joaquin Valley, California, where knowledge of its current status was limited or poorly understood. We used a trained detection-dog to survey for kit fox, red fox (V. vulpes), and gray fox (Urocyon cinereoargenteus) scats on selected properties, followed by species identification based on genetic analysis of DNA extracted from all scats collected. Despite extensive survey efforts (539 km), kit fox was only detected in Merced County, in the area of Santa Nella, where a small kit fox population was previously documented. Red fox scats were located in Alameda, San Joaquin, and Merced counties, and gray fox scats were located in Fresno County. Our results suggest that if kit foxes are present on the properties surveyed, they either occur at extremely low densities, rendering detection difficult, or only occur intermittently in these areas. In striking contrast, our previous surveys conducted with the same method in the southern part of the range found large numbers of kit fox scats in various areas, particularly in Kern and San Luis Obispo counties. We recommend that future conservation plans focus on preserving additional habitat in areas where kit foxes are relatively abundant, specifically western Kern County and the Ciervo-Panoche region.