We sequenced a 307-bp fragment of the mitochondrial cytochrome b gene from 42 individuals representing 14 populations of the western terrestrial garter snake, Thamnophis elegans. Current taxonomy recognizes either five or six subspecies of T. elegans based on color and scale morphology, but all agree on three major geographic races (T. e. elegans, terrestris, and vagrans). Although the cytochrome b phylogeny did not match subspecific classification of the populations, it did yield geographically proximate groups. Populations from the Sierra Nevada range and Monterey, California, formed one monophyletic group of T. e. elegans and T. e. terrestris. This Sierran/Monterey group was included in a larger group with eastern populations from the Great Basin (T. e. vagrans). The other well-supported group was comprised of populations from the western Great Basin (T. e. vagrans). One population from the northern California coast (T. e. terrestris) was basal to both groups of populations. Thus, neither T. e. vagrans nor T. e. terrestris formed monophyletic groups. Average percent sequence divergence between the outgroup (T. sirtalis) and T. elegans was 7.9–12%. Within T. elegans, divergence among populations ranged from 0.3–7.7%.