Coral reefs are increasingly threatened worldwide by a variety of biological and physical factors, including disease, bleaching and ocean acidification. Understanding levels of connectivity among widespread populations can assist in conservation efforts and the design of marine protected areas, as larval dispersal scales affect population demography. This study examined genetic connectivity and morphological variation of the broadcast spawning coral Montastraea cavernosa (L., 1767) among five locations in the Caribbean and Western Atlantic. Analysis of mtDNA and nuclear rRNA internal transcribed spacers, at both the local and regional scale, revealed that the majority of variation existed within locations rather than among them. Likewise, the majority of pairwise comparisons were non-significant between sites and locations. These results suggest that moderate to high gene flow occurs within and among populations of M. cavernosa in the Western Atlantic. The phylogeographic signature and significant pairwise comparisons among several locations, however, indicate that populations are also partially maintained through self-seeding and that gene flow may be restricted over large geographic distances. Additionally, while some anatomical variation is likely attributable to phenotypic plasticity, variations in skeletal morphology between Jamaica and other locations correspond with significant pairwise genetic distances and the presence of private sequence types (limited to a single location), suggesting selection to local environmental conditions.