Statistical analyses of occurrence data derived from new collections through scattered Caribbean sections indicate that increased speciation preceded a pulse of extinction during regional turnover of the Caribbean reef coral fauna in Plio-Pleistocene time. The data are based on samples that were newly collected and identified to species using standardized procedures. Age-dates were assigned using high-resolution chronostratigraphic methods. The results show that coral species with a wide range of ecological traits originated and were added to the species pool as much as 1-2 million years before extinction peaked at the end of turnover interval. Local assemblages consisted of a mix of extinct and living species, which varied in composition but not in richness. Extinction was selective and resulted in a faunal shift to the large, fast-growing species that dominate Caribbean reefs today. The unusual relationship between origination and extinction may have been caused by changes in oceanic circulation associated with emergence of the Central American Isthmus, followed by the onset of Northern Hemisphere glaciation. The pattern of origination preceding extinction may have been responsible for the stability of reef ecosystems during the intense climatic fluctuations of the late Pleistocene, and for the composition and structure of modern Caribbean reef ecosystems.