Historically, the Eastern Box Turtle (Terrapene c. carolina) was found in 31 counties in Michigan's Lower Peninsula, although it has been extirpated from 13 of those counties in the last ten years. One possible cause of the decline is road-based habitat fragmentation with resulting demographic and genetic consequences. Accurately identifying population structure is necessary to determine conservation units and aid in the recovery of Terrapene c. carolina. We genotyped 163 turtles at eight microsatellite loci from three locations in southwestern Michigan covering 360 km². We found high levels of genetic variation (H  =  0.83; A  =  16) and low levels of genetic differentiation (F_ST  =  0.006) in the system. The three areas exist as a single population and there was a low rate (11%) of misassignment across the sites. There was initial evidence of a genetic bottleneck in two of the three populations and the system as a whole. However, additional analysis failed to find a mode-shift in allele frequencies and did not detect any further evidence of a bottleneck in any of the populations. We conclude that the conflicting genetic indication of a bottleneck, despite the geographic evidence, is due to the long generation time of Terrapene c. carolina. Further, our study suggests that the retention of genetic variation despite population declines allows managers flexibility in dealing with the conservation of long-lived species.