We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. These data are from 102 individual Eastern Massasauga Rattlesnakes sampled at Bois Blanc Island, Michigan and genotyped at 15 microsatellite loci. Samples were collected as part of a study to examine functional connectivity for the Eastern Massasauga. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity.