Once widespread across the southern portion of California’s Central Valley, fewer than 5,000 federally endangered San Joaquin kit foxes (SJKF; Vulpes macrotis mutica) remain due to extensive habitat loss and fragmentation. Sarcoptic mange outbreaks in urban Bakersfield and Taft further threaten population persistence; however, the disease has not been observed outside urban areas or in other kit fox subspecies. Several SJKF populations are now small and isolated, increasing risks of extinction due to inbreeding or disease that may be compounded by historical loss of genetic diversity. We sequenced whole genomes from urban (n = 5) and non-urban (n = 12) SJKF populations and from desert kit foxes (DKF; V. m. mactrotis, n = 7), to assess past and present bottlenecks and characterize immune-gene variation (MHC, TLRs, IFNG, IL2). Demographic modeling revealed a severe, prolonged bottleneck in the SJKF population following divergence from DKF near the end of the Pleistocene, with variable recent inbreeding evident across the fragmented SJKF range. Genome-wide heterozygosity was lowest in the SJKF, and we found evidence for loss of genetic variation at immune-related genes. These results show how historical and contemporary demographic processes jointly constrain genomic health and may exacerbate disease vulnerability in this endangered subspecies.