Successful management of spatially isolated coral reefs is contingent on an understanding of ecological connections across populations. To investigate genetic connectivity of the depth-generalist coral species Montastraea cavernosa, populations from both shallow (15–30 m) and mesophotic coral ecosystems (30–70 m) in the Gulf of Mexico (GOM) were analyzed with microsatellite genotyping. A series of upstream and downstream sites were chosen in marine protected areas including Carrie Bow Cay, Belize; Flower Garden Banks and nearby mesophotic bank habitats; Pulley Ridge; and Dry Tortugas. Patterns of genetic diversity within the northwest GOM supported relatively open coral populations with high levels of gene flow between shallow and mesophotic depth zones, consistent with strong oceanographic patterns and hypothesized availability of coral reef habitats in the GOM. Conversely, genetic differentiation within Belize and the southeast GOM indicate relative isolation of shallow and mesophotic M. cavernosa populations in these regions. Structure analysis showed dominant genetic clusters within each region that did not correlate strongly with depth zones, and identified a cluster of unknown origin contributing to high differentiation at Pulley Ridge. Migration modeling predicted historical region-wide panmixia for most regions, with Pulley Ridge appearing to be a potential sink population. The GOM appears to demonstrate stronger evidence of vertical connectivity compared to elsewhere in the Tropical Western Atlantic, which may be the result of oceanographic variability and/or lack of local selection at depth. These findings are consistent with previous studies identifying genetic connectivity of broadcast-spawning corals across broad spatial scales and highlight the potential importance of mesophotic habitats in the GOM as larval sources to geographically distant populations.