The narrow-faced kangaroo rat (Dipodomys venustus) is endemic to the Coast Range of California. The three recognized subspecies are on the CDFW special animal list, however there is no formal protection. Among these, the Santa Cruz kangaroo rat (D. v. venustus) was only known to exist at a single location for the last ~20 years. A lack of information about the current distribution, population trends and genetic differentiation of the subspecies prevents further management action. We collected samples from live trapping and museum specimens to conduct a genomic study. Analyses of 168 individuals at 43,000 SNP loci clarified the species range and identified historical hybridization with the neighboring D. agilis. We identified six lineages within the species that are restricted to montane sky islands that are separated by areas of lower elevation and unsuitable habitat. Analyses of whole mitochondrial genomes revealed corresponding endemic clades that have been isolated since the last inter-glacial period (115-130 kya). We also identified finer scale population substructure consistent with habitat fragmentation. The lineages that we identified have a reduced geographic range, with reduced occupancy and increased fragmentation relative to historically. Our work has ramifications for the subspecific taxonomy within the species and conservation listing.