Geographic races of pocket gophers, Thomomys bottae, have been defined classically by differences in cranial dimensions, augmented by pelage color variation. Here, we distinguish between size and non-size related components of cranial variation and show that overall size is predicted mainly by features reflecting the nutritional quality of the available vegetation among the habitats occupied by gophers. Body size thus has a strong non-genetic, or environmental, basis. Cranial shape, on the other hand, identifies geographically homogeneous units that are concordant with electromorphically determined segments of the species' range. Cranial shape is, therefore, considered to represent underlying genetic influences and to identify more closely historical (phyletic) evolutionary units. In our view, these evolutionary units should form the basis for the infraspecific taxonomy of pocket gophers, and other organisms as well. The number of formal subspecies of T. bottae for the region of study (the deserts of eastern California) would be reduced from 11 to three by application of this criterion.