Tropical reef corals are ecologically important examples of mutualistic symbioses whose success is defined by the interwoven biologies of their symbiotic partners. These associations are exquisitely regulated, yet the equilibrium is sensitive to environmental disturbances, which cause a breakdown in symbiotic communication, loss of algae from the host, concomitant paling of coral coloration known as coral bleaching, and, if the conditions persist, death of the coral. Faced with the prospect of catastrophic coral mortality associated with global warming and related environmental shifts, researchers have focused their efforts on coral bleaching; although significant progress has been made in this area, understanding of the basic biology of these associations remains poor. Here we discuss several issues that have potentially contributed to this knowledge gap and conclude that without a sound understanding of the basic biology of these important symbioses, it will be very difficult to elucidate the mechanisms that drive coral bleaching.