Southwestern North America and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (Cophosaurus texanus) to examine range-wide diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population genomic and phylogenomic analyses support the existence of multiple lineages of C. texanus, with divergence following a southeast to northwest pattern. The geographic distribution of lineages, coupled with estimated divergence times, suggest a complex evolutionary history shaped by a combination of geomorphological shifts and ecological divergence in the Neogene. Our results also support the existence of a biogeographic barrier at the Continental Divide dating to the Pleistocene and the importance of isolation by distance. Migration rates between lineages are low, and species delimitation analyses further support the distinctiveness of lineages. Species tree analyses show that C. texanus texanus is nested within lineages of C. texanus scitulus, supporting the hypothesis that this system constitutes a species complex in need of revision. In sum, we find evidence for multiple processes influencing lineage divergence, indicating that additional multipronged phylogeographic studies using genomic data are needed on diverse, widespread taxa throughout arid western North America.