San Bernardino kangaroo rat (Dipodomys merriami parvus; SBKR), an endangered subspecies, faces ongoing anthropogenic threats such as habitat loss. Their habitat has undergone strong human-mediated fragmentation, resulting in extinction of some local populations and dramatic size reduction of the remaining populations. We examined the genetic diversity, population structure, and phylogeography of this subspecies using partial mitochrondrial DNA sequencing and microsatellite genotyping. Our study indicates that currently, the three remaining populations seem to be highly fragmented. Clear population structure and low level of haplotype sharing suggests that there has been no recent gene flow among populations, except in the case of human mediated gene flow as a result of a single translocation event. Diversity levels are on par with other species with fragmented distributions. Further, shallow phylogenetic divergence suggests the populations have not been diverged long enough to detect phylogenetic structure and separation is likely recent. Given the limited gene flow, low numbers of SBKR as evident by low return on trapping efforts, and low effective population size, habitat restoration and translocations may be warranted to maintain levels of diversity in a declining metapopulation.