Mass mortalities of reef-building corals have facilitated research on the mutualisms between cnidarians and their dinoflagellate endosymbionts. Competition experiments using three host-compatible symbionts found that while both the homologous native and the host-generalist symbiont cohabitated the host, each competitively dominated over a fast-proliferating symbiont from a different host species. At increased temperatures, the thermally sensitive native symbiont outcompeted the thermally tolerant non-native symbiont, indicating that co-evolved mutualisms are better adapted to function under stressful conditions.