The Diamond-backed Terrapin (Malaclemys terrapin), endemic to the brackish marshes of the eastern and Gulf of Mexico coasts of the United States, is a threatened species in Massachusetts with populations suffering drastic declines in the late 19th and early 20th centuries. To assess the potential effects of population bottlenecks on contemporary levels of genetic variation, we analyzed 219 bp of a major histocompatibility complex class I gene region (MHCI) by direct sequencing and single-strand conformational polymorphism analysis and six microsatellite loci from three locations around Cape Cod, Massachusetts. No variation was found at the MHCI, despite finding appreciable levels of variation within and among populations at the microsatellite loci. We discuss alternative explanations for these results, and we propose that the lack of variation at the MHCI may be due to the effects of selection rather than demographic changes in terrapin populations.