Dorsal pelage color, morphometry of cranial characteristics, and sequences of 500 base pairs from mitochondrial cytochrome-b gene of pocket gophers (Thomomys bottae) from the Cape region in Baja California Sur were used to evaluate how the environment influences morphologic and genetic structure in populations from habitats with altitudinal segregation. Gophers from temperate forest, tropical deciduous forest, and desert scrub were sampled. Among 80 individuals examined, 34 haplotypes were found. Specimens collected in each habitat were not monophyletic. Analysis of molecular variance indicated that more than one-half of the total pool of genetic variation was contained among individuals within local populations and that only 0.6% could be explained by the different habitats; there was no genetic structure and the populations were genetically similar. Individuals in the temperate forest were larger, darker, and more diverse in coloration; individuals from tropical deciduous forest were smaller; and those from desert scrub had lighter coloration. There were no differences among populations in cranial shape. Only the dorsal coloration of the specimens from the temperate forest matched the color of moist soil. There were no diagnostic characteristics to recognize T. b. alticolus, the population restricted to high-elevation temperate forests in La Sierra de La Laguna, as a valid subspecies; we consider it a junior synonym of T. b. anitae. The range of this subspecies is from the San Ignacio Lagoon to the southern end of the Baja California peninsula.