Today the coral faunas, reef development, and reef morphologies differ substantially on the Caribbean and Pacific coasts of the Central American isthmus. The contemporary eastern Pacific reef-building coral fauna consists of ~45 species and the Caribbean ~75 species with Porites the only genus common to the two regions. Zooxanthellate coral richness reached 55 species during the early Oligocene epoch, ~30 Ma, and then steadily declined until Holocene time, 11–12,000 years ago. Species of the fire coral genus Millepora have been recently discovered in the eastern Pacific, all of Indo-Pacific identities and with restricted distributions (Gulf of Chiriquí, Panama, and Clipperton Atoll). Reef development is robust and widespread in the Caribbean and less strong (particularly among Pocillopora reefs), and often confined to sheltered areas in the eastern Pacific. Western Atlantic and eastern Pacific coral faunas were continuous, the same, during most of Cenozoic time but became separated with the emergence of the Central American land bridge about 3 Ma. Morphometric and molecular evidence support a strong genetic affinity between eastern Pacific and Caribbean Porites species, indicating local speciation (vicariance premise) and a frequent influx of Indo-Pacific species via long distance larval transport during strong El Niño eventsEl Niño events (1982–83, 1997–98) (dispersal premise). The tropical “eastern Pacific barrier”, the wide expanse of deep, open ocean waters preventing the dispersal of shallow marine organisms, is porous and best regarded as a filter bridge. Nearly all recent eastern Pacific coral species resulting from dispersal (88%) greatly outnumber endemic species (12%).