The enduring processes of time, climate, and adaptation have sculpted the distribution of organisms we observe in the Sonoran Desert. One such organism is Morafka’s desert tortoise, Gopherus morafkai. We apply a genomic approach to identify the evolutionary processes driving diversity in this species and present preliminary findings and emerging hypotheses. The Sonoran Desert form of the tortoise exhibits a continuum of genetic similarity spanning 850 km of Sonoran desertscrub extending from Empalme, Sonora, to Kingman, Arizona. However, at the ecotone between desertscrub and foothills thornscrub we identify a distinct, Sinaloan lineage and this occurrence suggests a more complex evolutionary history for G. morafkai. By using multiple loci from throughout the tortoise’s genome, we aim to determine if divergence between these lineages occurred in allopatry, and further to investigate for signatures of past or current genetic introgression. This international, collaborative project will assist state and federal agencies in developing management strategies that best preserve the evolutionary potential of Morafka’s desert tortoise. Ultimately, an understanding of the evolutionary history of desert tortoises will not only clarify the forces that have driven the divergence in this group, but also contribute to our knowledge of the biogeographic history of the Southwestern deserts and how diversity is maintained within them.