Previous population genetic studies of diamondback terrapins (Malaclemys terrapin) have typically focused on either the entire range or relatively small spatial scales. The Louisiana coastline contains vast salt marshes suitable for terrapins; however, two major freshwater inputs (Atchafalaya River and Mississippi River Deltas) break up the seemingly contiguous habitat and may isolate populations of terrapins. To determine population genetic structure and connectivity of terrapins occupying Louisiana marshes, we collected 573 individuals from 26 study sites across the Louisiana coastline. Twelve microsatellite loci were used to evaluate population structure using standard genetic and spatially explicit approaches. Patterns of gene flow were examined via model testing, including those to determine if freshwater inputs serve as barriers to movement. We also assessed levels of genetic diversity, inferred the historical demography and estimated effective population sizes across our sampling. While we did not detect significant population structure, we found that terrapins are not panmictic, and demonstrated a pattern of isolation by distance along the Louisiana coastline. Genetic diversity in this study was comparable to the Atlantic coast, but was higher than other sites within the Gulf of Mexico. Though terrapins in eastern Louisiana were historically harvested and apparently experienced a genetic bottleneck, this is not reflected in estimates of effective population sizes. Although, there was no strong genetic structuring across Louisiana, historical differences and patterns of habitat loss suggest that it may be necessary to develop separate management strategies for the western and eastern portions of the state.