A large number of coral species in the Caribbean Sea disappeared in the early Miocene. Based on climate model simulations, we propose that this regional extinction is related to a flow reorganization in the Panama Seaway. It is shown that large-scale tectonic events, such as the opening of Drake Passage and the closing of the Tethys Seaway, reorganized the global ocean currents to induce a reversal of the volume transport between Atlantic and Pacific. This flow reversal, which is timed near the Oligocene-Miocene boundary, allowed cool Pacific waters to enter the Caribbean Sea possibly affecting the habitat of warm water tolerant coral species.