Destruction and fragmentation of wildlife habitat often results in small, isolated populations that are highly susceptible to extirpation. In many cases, however, estimates of population size are lacking, precluding accurate assessments of population viability and sound conservation management recommendations. The Eastern Massasauga (Sistrurus catenatus) is a federally threatened pitviper species that has been extirpated throughout much of its historic range attributable to agricultural conversion of wetland habitat and other synergistic threats. Population size is generally unknown among extant massasauga populations, making site-specific management difficult. In this study, we estimated genetic effective population size (N_e) and census population size (N_c) for Eastern Massasaugas at two sites in southwest Michigan. For each population, we used mark–recapture models to estimate N_c and the linkage disequilibrium method to estimate N_e. Our results revealed small N_c, with approximately 108 (95% CI = 87–165) and 148 (95% CI = 102–295) adults estimated at our study sites in Cass County and Barry County, respectively. Estimates of N_e were even smaller: approximately 29.5 (95% CI = 21.2–43.1) for Cass County and 44.2 (95% CI = 30.8–69.3) for Barry County. Additionally, N_e/N_c ratios were similar across study sites, suggesting some stability in this ratio for Eastern Massasaugas, at least for populations in close proximity. Although we did not detect high levels of inbreeding or relatedness in either population, we caution that these small populations could become increasingly vulnerable to extirpation from unpredictable threats such as disease and climate change.