The Western Massasauga (Sistrurus tergeminus) is a small, North American rattlesnake found west of the Mississippi River. Sistrurustergeminushas previously been divided into two putative subspecies, Desert (S. t. edwardsii) and Prairie Massasaugas (S. t. tergeminus) based upon qualitative variation in morphology, coloration, and habitat. The Desert Massasauga subspecies has been formally petitioned for federal listing under the U.S. Endangered Species Act. Ouroverarching goal was to evaluate genetic structure and genomic differentiation between specimens of the two putative subspecies in an effort to inform ongoing conservation assessments. To that end, we generated whole genome sequence data for both putativetaxa and then developed nearly 200 genetic markers from different fractions of the genome (~50 intergenic and ~50 genic markers from each of the two subspecies) to test for population structure across much of the Western Massasauga range. Mean genomic divergence between subspecies was only 0.0041 ± 0.0080 (Kimura’s 2-parameter distance) for nuclear sequences and 0.0175 ± 0.0031 for mitochondrial sequences, both exceedingly low values which approach the minimum of zero. Admixture analyses and F-statistics both indicated that regardless of how the markers were partitioned, genetic structure was oriented far more along a geographic axis (isolation-by-distance) than a taxonomic axis (i.e., between putative subspecies). Overall, our analyses provide little support that formal protection of the purported Desert Massasauga is warranted based on the homogeneity of the collective Western Massasauga gene pool.