The San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is a federally endangered species. Today, fewer than 5,000 individuals are thought to occur across their range, and the contemporary metapopulation is distributed across three core regions and several smaller satellite populations. While anthropogenic habitat loss is believed to be the fundamental cause of the historical decline of the SJKF, localized disease outbreaks today proximately threaten remaining populations both demographically and genetically. For example, in the last decade, sarcoptic mange has caused significant declines in a formerly abundant urban SJKF population in Bakersfield. As part of a broader range-wide genomic study, we present data comparing the genetic diversity of SJKF in Bakersfield before and after the mange outbreak. We used reduced-representation genomic sequencing to compare population structure, landscape connectivity, and local genetic diversity of historical SJKF individuals sampled prior to the mange outbreak (n = 57) as well as of individuals sampled from the contemporary population (n = 95), focusing on both urban (n = 54) and exurban (n = 98) regions.