Elevational gradients coincide with expansive climatic gradients and diverse plant and animal communities. We evaluated the small mammal assemblages in eight distinct vegetation types across an elevational gradient in southern California, the Deep Canyon Transect, to determine how assemblage composition changes across the gradient and to identify species with similar habitat associations. Livetrapping efforts (4,800 trap-nights) yielded 1,097 captures of 713 individuals, representing 14 heteromyid and cricetid species. Heteromyids dominated the six lower-elevation vegetation types (< 1,300 m a.s.l.), whereas cricetids dominated the upper end of the gradient. Richness and diversity exhibited bimodal responses to elevation, which do not conform to mid-domain effect null predictions. Canonical correspondence analysis revealed that 75% of the variation in small mammal abundances was explainable by habitat characteristics, and cluster analysis grouped small mammals into three ecologically distinct groups based on their habitat associations. One contained only Chaetodipus penicillatus, while the others were comprised of low- and high-elevation species, respectively. The low-elevation species exhibit unusual levels of sympatry (and syntopy) among closely related species of pocket mice (Chaetodipus). Further efforts should investigate the mechanisms of coexistence for Chaetodipus species with nearly identical associations and seasonal effects on richness and diversity. Repeated surveys of entire gradients such as the Deep Canyon Transect will help refine our understanding of temporal dynamics of community assemblage and diversity.