The persistence of scleractinian coral populations on the Florida Reef Tract (FRT) is controlled in part by metapopulation dynamics and larval dispersal. Nine polymorphic microsatellite loci were analyzed to characterize contemporary population structure and gene flow as well as historical migration rates of Montastraea cavernosa at five sites off Martin, Palm Beach, and Broward counties in southeast Florida. The sampled populations demonstrated evidence of genetic isolation by distance over a geographic range of 85 km. Population genetic structure was divided into two genetic clusters, northern and southern, with admixture along a latitudinal gradient. Historical migration models indicated likely panmixia throughout all sites sampled, identifying a potential reduction in connectivity among the sampled populations through time. Though M. cavernosa populations demonstrated evidence of historical connectivity, contemporary patterns of isolation by distance suggest that effective management will require localized actions to maximize the likelihood of sustaining individual populations in the northern FRT. Given the results of this study, coupled with recent coral mortality events in the region, we recommend regional conservation efforts and management initiatives throughout southeast Florida within a more comprehensive FRT-wide management network.