Tropical and subtropical marine ecosystems are noted for the diversity of their fauna and flora and particularly for the coral reefs which directly and indirectly provide food, habitat, and other resources in what have been considered to be nutrient-poor waters. The scleractinian corals and coralline algae form the structural and functional basis of the reefs. Thus, the demise of these organisms in many localities has brought concern about their fate and that of the other species they support. Beginning in the mid-1970s, several diseases of corals were recognized. Black-band and red-band diseases result from the formation of mats consisting of consortia of cyanobacteria and other microbes that produce hydrogen sulfide and anoxia to cause the death of the coral. Rapid tissue loss (a few millimeters to centimeters per day) has also been observed in what are known as white-band disease, white plague, and white pox, but the causes of these diseases are still under investigation. Yellow-blotch and yellow-band diseases, in which a patch or margin of yellowish-lightened tissue appears on the surface of some species of corals, have reached epizootic levels on some reefs. Bleaching, loss of the corals’ symbiotic algae or algal pigments, has occurred globally. Coralline algae have succumbed to coralline lethal disease and coralline lethal orange disease. Diseases that are suspected to be caused by pathogens have also affected other reef species, including sponges, gorgonians, giant clams, and echinoderms. The most extensive epizootic known in marine ecosystems reduced populations of the Caribbean long-spined sea urchin by 85–100 percent. As in other organisms, the roles of pathogens and abiotic factors are undoubtedly tightly interlinked. Changes in water quality, such as increased nutrient, chemical, and sediment loading, extremes in temperature and salinity, and increased ultraviolet radiation, are believed to be altering the susceptibility of reef organisms to parasites and pathogens. Continuing research on the causal agents of disease in corals, coralline algae, and other reef invertebrates should improve our understanding of these interactions and suggest potential management options for protecting these important organisms and the coral reef ecosystem.