Larval connectivity among and within coral reefs is important for sustaining coral metapopulations, enhancing ecosystem resilience through species and genetic diversity, and maintaining reef ecosystems' structure and functions. This study characterized genetic structure and assessed horizontal and vertical connectivity among populations of the ubiquitous gonochoric broadcast spawning coral Montastraea cavernosa in Belize. Using nine polymorphic microsatellite loci, we genotyped M. cavernosa colonies from four depth zones at four study sites within Belizean marine management zones. Study sites were selected within South Water Caye Marine Reserve (3 sites) and Glover's Reef Marine Reserve (1 site). Strong contemporary genetic differentiation was observed between relatively shallow M. cavernosa populations (10 m, 16 m) and relatively deep (25 m, 35 m) populations, coinciding with a transition from reef crest to reef slope. These results were consistent across both marine reserves. Vertical and horizontal migration models suggest that all populations were historically panmictic, with little unidirectional migration. The relative local isolation of shallow and mesophotic M. cavernosa populations in Belize, coupled with the importance of Belize's upper mesophotic populations as potential larval sources for other areas in the Tropical Western Atlantic, reinforces the need for management strategies that conserve coral populations across all depth zones.