To investigate morphological variation of cranial elements in western massasauga (Sistrurus tergeminus) populations, we obtained microCT scans from 121 wet-preserved individuals representing 10 populations across the U.S. and Mexico. We developed landmark schemes of dorsal and lateral skull orientations that capture major aspects of skull shape and account for snake skull kinesis, then Procrustes superimposed landmarks to translate, rotate, and scale the schemes. We ordinated the landmarks with a principal components analysis and used linear discriminant functions to test the reliability of taxonomic, population, and sex assignments. PC1 (~42.9% explained variance) represents an axis of nasal and premaxilla compression and braincase and occipital region elongation, potentially associated with among-population dietary differences. PC2 (~9.7% explained variance) represents lengthening of the supratemporal bone, associated with viperid striking and feeding mechanisms, in northern populations. Discriminant functions classified individuals to S.t. tergeminus and S.t. edwardsii with 77.1% and 62.8% accuracy, respectively. Males and females were less accurate, with 66.7% and 49.0% accuracy, respectively, suggesting more geographic variation than sexual dimorphism. The classification accuracy of specific populations was low, at 28.1%, however, populations were assigned to other geographically close populations. Further investigation into the differences between diet and other ecological factors across the geographic distribution of S. tergeminus populations will help reveal the specific factors associated with identified morphological differences.