Scleractinian coral evolution is often characterized by alternating patterns of lineage diversification and fusion, thus leading to reticulate evolution. Although this pattern is hypothesized in many coral lineages, including the Montastraea annularis species complex, it is not known what effects cladogenesis and hybridization have on the symbioses between corals and their endosymbiotic dinoflagellates (genus Symbiodinium). To explore this, the genetic diversity of M. faveolata and M. annularis in the Upper Florida Keys, USA, and Exuma Cays, The Bahamas, was examined using a mtDNA intergenic region. The host genotypic data were then analyzed in relation to the diversity of the corals' Symbiodinium communities as determined by internal transcribed spacer region 2 (ITS2) and 3 microsatellite markers specific to Symbiodinium Clade B. M. faveolata and M. annularis in the Upper Florida Keys were genetically distinct from one another while these coral species in the Exuma Cays shared mtDNA haplotypes. These findings suggest possible regional differences in the degree of intergressive hybridization between M. faveolata and M. annularis. When Symbiodinium diversity was examined, Montastraea spp. from both regions shared Symbiodinium ITS2 genotypes; however, host-symbiont specificity was observed using higher resolution microsatellite markers. Specifically, M. faveolata and M. annularis from the Upper Florida Keys all harbored genetically distinct multilocus Clade B genotypes, whereas these 2 coral species in the Exuma Cays shared Clade B genotypes. Consequently, the degree of fine-scale specificity between Symbiodinium Clade B genotypes and Montastraea spp. appears to be governed by the degree of genetic distinction, and possibly hybridization, between these host 'species'. © Inter-Research 2010.