Abstract.•The three members of the Montastraea annularis complex (M. annularis, M. franksi, and M. faveolata) are dominant reef builders in the western Atlantic whose species status has been controversial for over a decade. Although differences in colony morphology and reproductive characteristics exist, interspecific fertilizations are possible in the laboratory and genetic differentiation is slight. Here we compare the three taxa genetically and morphologically in Panama and the Bahamas, widely separated locations spanning most of their geographic ranges. In Panama, analyses of three AFLP loci, a noncoding region of the mitochondrial genome, and ITS sequences reveal that M. faveolata is strongly differentiated genetically. Discriminant function analysis also indicates no overlap with the other two species in the fine structure of the corallites that comprise the colony. Genetic analyses of larvae from interspecific crosses between M. faveolata and the other two taxa confirmed the hybrid status of the larvae, but no examples of the most probable Fi genotype were observed in the field. Although M. annularis and M. franksi were more similar, they also exhibited strong frequency differences at two AFLP loci and in the mitochondrial noncoding region, as well as distinct corallite structure. In the Bahamas, in contrast, the three taxa exhibited overlapping morphologies. Montastraea franksi and M. annularis were indistinguishable genetically, and M. faveolata was distinct at fewer genetic loci. Once again, however, the most probable Fi genotype involving M. faveolata was not observed. Geographic differences between Panama and the Bahamas explain why past studies have come to different conclusions concerning the status of the three species. In general, the genetic and morphological data suggest a north to south hybridization gradient, with evidence for introgression strongest in the north. However, reproductive data show no such trend, with intrinsic barriers to gene flow comparable or stronger in the north. However, it has proved difficult to find genetic differences accepted for plants but appears to be more limited in animals among these taxa using DNA sequence data. For example, (Arnold 1997; Dowling and Secor 1997); thus corals repre-analyses of the ITS regions of rDNA, an intron in the Bsent an important model in this regard.tubulin gene, and mitochondrial COI sequences showed no The Montastraea annularis complex lies at the heart of this fixed DNA sequence differences among them (Lopez and debate. Its three putative species (M. annularis, M. faveolata, Knowlton 1997;Medina et al. 1999). More recently, however, and M. franksi) are ecologically dominant, broadly sympatric, one amplified fragment length polymorphism (AFLP) locus and often in close proximity on many tropical western At-was identified that distinguished M. faveolata from the other lantic reefs. For many years, it was thought that these three two taxa (Lopez et al. 1999), and sequence analysis confirmed morphotypes represented intraspecific variation...