Sidewinder Rattlesnakes (Crotalus cerastes) are morphologically and genetically variable denizens of the North American warm deserts. However, current taxonomy based in morphology is incongruent with mitochondrial genetic structure. To reconcile this, I generated a large genomic dataset to identify three genomic clusters of individuals within C. cerastes. I utilized geometric morphometrics, an innovative method of quantifying shape, to identify morphological variation across the range of C. cerastes. Finally, I compared a genomic method of species delimitation (STACEY) with a simultaneous species delimitation using both genomic and morphological data, assessed relative contribution of the data to the analysis, and applied a genealogical divergence index (gdi) to demonstrate the existence of a cryptic species of C. cerastes in southern Sonora, MX.