The corals Acropora palmata and A. cervicornis are important Caribbean reef-builders that have faced significant mortality in recent decades. While many studies have focused on the recent demise of these species, data from areas where Acropora spp. have continued to thrive are limited. Understanding the genetic diversity, recruitment, and temporal continuity of healthy populations of these threatened Acropora spp. and the hybrid they form (''Acropora prolifera'') may provide insights into the demographic processes governing them. We studied three reef sites with abundant A. cervicornis, A. palmata, and hybrid Acropora populations offshore of Ambergris Caye, Belize at Coral Gardens, Manatee Channel, and Rocky Point. Samples were collected from all three Acropora taxa. We used microsatellite markers to determine: (1) genotypic diversity; (2) dominant reproductive mode supporting local recruitment; (3) minimum and maximum genet age estimates for all three acroporids; and (4) the history of hybrid colonization at these sites. We found that Acropora populations were highly clonal with local recruitment primarily occurring through asexual fragmentation. We also estimated the ages of 10 Acropora genets using recent methodology based on somatic mutation rates from genetic data. Results indicate minimum ages of 62-409 yr for A. cervicornis, 187-561 yr for A. palmata, and 156-281 yr for the Acropora hybrids at these sites. Our data indicate that existing A. cervicornis, A. palmata, and Acropora hybrid genets persisted during the 1980s Caribbean-wide Acropora spp. collapse, suggesting that these sites have been a refuge for Caribbean Acropora corals. Additionally, our data suggest that formation of extant hybrid Acropora genets pre-dates the widespread collapse of the parent taxa.