Understanding how habitat heterogeneity influences the genetic structure of populations is an important goal of conservation genetics. Species with different evolutionary histories may respond differently to contemporary habitat loss and fragmentation. Recent genetic analyses have shown high levels of genetic structure in two subspecies of Massasauga Rattlesnakes of conservation concern (Eastern Massasaugas, Sistrurus catenatus catenatus and Desert Massasaugas, Sistrurus catenatus edwardsii) living in highly fragmented habitats. Here, we complement those results with an analysis of the genetic structure of the third subspecies (Western Massasaugas, Sistrurus catenatus tergeminus), which has a largely continuous distribution in Kansas but with some isolated populations in Missouri. We found no evidence of genetic structure among the Kansas populations of Western Massasaugas, though our STRUCTURE analysis did identify the two Missouri populations as distinct clusters from each other and from the Kansas populations. Population differentiation estimates were much lower across all Western Massasauga populations compared to those observed in Eastern and Desert Massasaugas. Quantitative analyses of habitat availability and fragmentation confirm that the Kansas landscape is less fragmented than the range occupied by Eastern Massasaugas; this supports a possible influence of habitat fragmentation on genetic structure of these snakes. The more-continuous distribution and relative genetic uniformity of Western Massasaugas found in Kansas contrast with the isolated nature of Desert and Eastern Massasaugas, making the Western subspecies unique within the Massasauga complex.