The Heermann's kangaroo rat (Dipodomys heermanni; Rodentia: Heteromyidae) is a Californian endemic primarily found in the dry, gravelly grassland and open chaparral habitats of the San Joaquin Valley. Current taxonomy (based on morphology and habitat use) recognizes nine subspecies within this kangaroo rat species. Management practices of D. heermanni primarily are based on this classification, but this taxonomy may not accurately reflect unique lineages in need of conservation. Using molecular and morphological data, we performed a phylogeographic assessment of D. heermanni across the full geographic range of the species. Phylogenetic and network analyses of mitochondrial data from over 90 museum specimens (representing all nine subspecies distributed across the range of the species) revealed no substantial genetic differentiation within D. heermanni. Similarly, a geometric morphometric analysis of the crania of over 200 adult D. heermanni museum specimens (again representing all subspecies across the geographic distribution of species) resulted in no apparent morphological clustering across geography. Our results indicate that recognition of none of the nine subspecies is warranted and that conservation and management practices of D. heermanni are in need of revision.