We used genomic SNPs to study introgression and phylogeography in two Massasauga (Sistrurus spp.) contact zones in the midwestern and southwestern United States. We explored the paraphyletic relationships seen within Sistrurus tergeminus tergeminus and S. t. edwardsii as well as potential hybrids in a disjunct population of S. tergeminus in Missouri. Our data support contrasting biogeographic factors to have modulated the evolutionary history of Sistrurus tergeminus. In the Midwest, glacial cycles likely facilitated introgression via alternating periods of isolation and secondary contact, coupled with undulating physiographic features. Furthermore, we identified cryptic population structure within S. t. tergeminus that may warrant conservation consideration, whereas the disjunct Missouri population situated between the main S. tergeminus and S. catenatus ranges shows genetic signals of secondary contact and may represent a relictual lineage. In the southwestern contact zone, S. t. tergeminus and S. t. edwardsii may be undergoing primary divergence, accordant with the more limited presence of physiographic barriers in the region and the lower genetic divergence observed among the two taxa.