Regional anthropogenic processes such as pollution, dredging, and overfishing on coral reefs currently threaten the biodiversity of stony corals and other reef-associated organisms. Global climate change may interact with anthropogenic processes to create additional impacts on coral diversity in the near future. In order to predict these changes, it is necessary to understand the magnitude and causes of variation in scleractinian coral diversity throughout their 240 million year history. The fossil record documents long periods of speciation in corals, interrupted repeatedly by events of mass extinction. Some of these events relate clearly to changes in global climate. Diversity in reef corals has increased since their last period of extinction at the end of the Cretaceous (65 My bp), and is still rising. During the last 8 million years, the fragmentation of the once pantropical Tethys Sea separated corals into two major biogeographical provinces. Periods of glaciation also have caused major changes in sea level and temperature. Accumulated evidence supports the theory that relative habitat area and changing patterns of oceanic circulation are mainly responsible for the two observed centres of recent coral diversity at the western tropical margins of the Atlantic and Pacific oceans. At predicted rates of climate change in the near future, coral reefs are likely to survive as an ecosystem. Increases in sea level may actually benefit corals and lead to regional increases in diversity if new habitat area on back reefs is opened to increased water circulation and thus coral dispersal. Rising temperature may cause higher rates of coral mortality and even local extinction in isolated, small populations such as those on oceanic islands. The effects of increases in ultraviolet radiation (UV) are largely unknown, but likely to be negative. UV may damage planktonic coral propagules in oceanic surface waters and thus decrease rates of gene flow between coral populations. This may result in increased local extinctions, again with the strongest impact on widely separated reefs with small coral populations. The largest threats to coral diversity are regional anthropogenic impacts, which may interact with global climate change to exacerbate rates of local species extinctions. Centres of high reef coral diversity coincide with human population centres in south-east Asia and the Caribbean, and thus the greatest potential for species loss lies in these geographical areas.