Using a novel molecular biomaker system (MBS), we assessed the physiological status of coral (Montastraea faveolata) challenged by heat stress by assaying specific cellular and molecular parameters. This technology is particularly relevant for corals because heat stress is thought to be an essential component of coral bleaching. This phenomenon is widely believed to be responsible for coral mortality worldwide, particularly during 1997–1998. Specific parameters of coral cellular physiology were assayed using the MBS that are indicative of a nonstressed or stressed condition. The MBS distinguished the separate and combined effects of heat and light on the 2 coral symbionts, a scleractinian coral and a dinoflagellate algae (zooxanthellae). This technology aids in the accurate diagnosis of coral condition because each parameter is physiologically well understood. Finally, the MBS technology is relatively inexpensive, easy to implement, and precise, and it can be quickly adapted to a high-throughout robotic system for mass sample analysis.