Coral reefs worldwide have become increasingly affected by a phenomenon known as "coral bleaching," the loss of the symbiotic algae from the host corals. The underlying causes and mechanism(s) of coral bleaching are not well known, although several have been hypothesized. While coral bleaching has been a primary focus in recent years, corals respond differentially to numerous environmental stresses. The impacts of heat, hydrocarbons, salinity, sewage effluents, biocides, heavy metals, and ultraviolet light have been investigated in both laboratory experiments and field surveys among multiple coral species. Herein what is known regarding the biological impacts of such stresses on corals at the molecular level of organization is summarized. The objective is to focus attention at the early stages of biological effects in order to encourage and facilitate research that provide ways to understand how changes at the molecular level might elucidate processes likely occurring at the population level. This, in turn, should accelerate studies that may elucidate the cellular and physiological changes contributing to coral decline, rather than just document the continued global loss of coral diversity and abundance.