Historical subspecies often serve as important units for conservation policy and management when other information is lacking. However, adaptive management of sensitive species is compelled to rely on the best scientific data available, making accurate delineation of lineage diversity an important and enduring task. The California glossy snake, Arizona elegans occidentalis is currently recognized as a Species of Special Concern in California due to rangewide decline and projected effects of anthropogenic development throughout the range. To test whether A. e. occidentalis forms a cohesive group, we used genomic analyses combined with an expanded taxonomic and geographic sampling scheme across the species. We show strong genomic evidence for recognizing a new species, Arizona occidentalis, that encompasses all of the formerly recognized subspecies of the so-called “short-tailed glossy snakes”, and is the sister species to Arizona pacata, the endemic species in Baja California. We retain the name Arizona elegans for the “long-tailed glossy snakes” in the eastern portion of the complex’s range. Within Arizona occidentalis, we show support for regional genetic partitioning into San Joaquin, Mojave and Sonoran Desert groups and discuss whether one or more of these groups merit recognition as Distinct Population Segments as defined in the Endangered Species Act of 1973, given the on-going habitat loss along the western edge of its range.