A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread garter snake Thamnophis elegans to quantify the influence of historical biogeography and environmental variation on patterns of genetic diversity. We used genotyping-by-sequencing to assess patterns of dispersal and vicariance across biogeographic regions using ancestral area reconstruction, and population connectivity using estimated effective migration surfaces. We also identified environmental variables potentially shaping local adaptation in regional lineages using genetic-environment association (GEA) analyses. Our analyses recovered three well-differentiated genetic groups corresponding to three subspecies (T. e. elegans, T. e. terrestris, and T. e. vagrans) and a general eastern to western dispersal history across western North America. Fine-scale spatial structure was explained by geographic features and potential local adaptation in both T. e. elegans and T. e. terrestris. Populations of T. e. elegans displayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations of T. e. terrestris show discrete genetic breaks consistent with well-known biogeographic barriers. GEA analyses suggest that local adaptation due to a common set of environmental variables has further shaped spatial patterns of genetic variation in T. e. elegans and T. e. terrestris. We recovered stark genetic differentiation among and within three subspecies of T. elegans. Subspecies T. e. elegans and T. e. terrestris show distinct patterns of diversification while adapting to the new environments they colonized.