Reef corals are especially sensitive to environmental change since their survival is dependent on a delicate balance between the coral host and its algal endosymbiont. Predicting the responses of reef ecosystems to global climate change requires a detailed understanding of the diversity of both partners in this symbiosis. The current perception of coral-inhabiting symbiont diversity at nuclear ribosomal DNA is shown in this issue of Molecular Ecology to be a significant underestimate of the wide diversity that in fact exists. Apprill & Gates (2007) reveal eight- to tenfold greater diversity than previous methods had identified. The authors underline the importance of detailed knowledge of such diversity if we are to predict, or possibly manage, the acclimatization and adaptation of reef corals to climatic change.