Fewer than 5,000 federally endangered San Joaquin kit fox (Vulpes macrotis mutica) remain, largely due to habitat loss and fragmentation. Additionally, sarcoptic mange outbreaks in Bakersfield and Taft threaten these urban populations. To date, sarcoptic mange infestations have not been documented outside of the urban areas despite extensive surveillance, nor has it been observed in any other kit fox subspecies. We identified several non-urban populations that are relatively isolated and may be at increased risk of extinction due to inbreeding or disease. To assess the genomic impacts of fragmentation and disease, we sequenced whole genomes from kit foxes samples in urban (n = 5) and non-urban (n = 12) populations, comparing levels of inbreeding and genetic load. We also investigated immune-related genetic diversity (e.g., MHC, IFNG, IL2) between urban and non-urban populations, and between the San Joaquin kit fox and individuals from the closely related desert kit fox subspecies (n = 7), to explore potential links to sarcoptic mange susceptibility. Our findings provide insights into how genetic diversity and population connectivity may influence disease vulnerability and persistence in this endangered species.