Corals engage in relationships with prokaryotic microorganisms which are thought to play important roles in coral health. However, the significance of most coral endosymbionts has remained elusive, and this is partially attributed to the complexity of the symbioses across the biogeochemically diverse mucus, tissue and skeletal microenvironments of the coral and the fact that corals readily feed on microbes. Here I present DNA and microscopy-based evidence from studies of Caribbean and Pacific corals that demonstrates that corals do harbor specific tissue-associated, putative endosymbiontic bacteria and archaea, including common symbionts of other marine invertebrates. I will describe the potential significance of these relationships and our ongoing efforts to elucidate the role of the coral-associated prokaryotes in host health. I will also briefly discuss our recent collaboration with Cuban coral reef scientists, and our efforts to extend microbiome investigations to the corals of Cuba.