Montastraea annularis, M. franksi and M. faveolata are a complex of recently distinguished coral species whose status remains controversial due to the lack of fixed differences. Here we report on two types of genetic analyses for these taxa: 1) DNA sequences of two nuclear genes [internal transcribed spacers of rDNA (ITS-1, ITS-2) and a ɮ-tubulin intron] and 2) a preliminary screening of the entire nuclear genome using amplified fragment length polymorphisms (AFLP). There was very little variation within or among the three species in DNA sequences. Onlly 3 of 300 nucleotide positions in ITS-1, 3 of the 350 positions in ITS-2, and 3 of 350 positions in the ɮ-tubulin intron had large amounts of polymorphism. At some of these sites there were allele frequency differences among the species, but no diagnostic substitutions. Sequences from polymorphic sites in the ɮ-tubulin intron also showed evidence of heterozygosity. Pilot experiments with AFLP yielded stronger evidence of genetic boundaries among these species. Two AFLP primers gave patterns of band presence or absence that were potentially diagnostic for M. faveolata (n=7) versus M. franksi (n=7); M. annularis (n=4) may also have diagnostic patterns, but the differences between it and M. franksi were quantitative (band intensity) rather than qualitative.