Coral skeletons harbor diverse assemblages of endolithic microorganisms that often have a profound influence on the ecology and physiology of the coral host. While the cyanobacterial and eukaryotic microalgal components of these endolithic assemblages are well characterized, information on the other components remains scarce. Here, we characterize the endolithic microbial assemblages in the skeleton of the massive coral Goniastrea aspera in both oligotrohic and eutrophic environments. In addition to the green bands typically found in massive coral skeletons, multiple black bands were observed in skeletons from oligotrophic waters. Sequence analysis of the dsrB (dissimilatroy sulfite reductase beta-subunit) gene revealed that colonies with black bands harbor a diverse assemblage of sulfate-reducing bacteria (SRB). In contrast, SRB were not detected in skeletons from eutrophic waters. We conclude that increases in nutrients may have an important effect on the microbial assemblages residing within coral skeletons.