We examined geographic trends in 4 morphological data sets (both craniodental and colorimetric measurements and scores of cranial foramina and qualitative craniodental variables) within and among 5 subspecies of the California vole, Microtus californicus, that occur within or adjacent to the Mojave Desert in eastern California. These analyses are corollary to those previously published on the same samples using both mitochondrial and nuclear gene sequences and microsatellite loci. The morphological and molecular data sets are generally concordant in supporting the existing infraspecific taxonomy, although important conflicts are evident. With the combination of data sets, we are able to assign previously unknown samples to these infraspecific taxa. We define and provide an emended diagnosis of each subspecies using the criteria established by Willi Hennig in his 1966 assessment of the qualities and characteristics of infraspecific taxa, which he understood to be fundamentally different than the hierarchical phylogenetic system he established as the conceptual framework for taxa at the species level and above. Hennig’s views are contrary to how the subspecies concept has been applied in much of recent mammalian taxonomy.