Coral reefs in the Tropical Eastern Pacific (TEP) are among the most isolated in the world. This isolation has resulted in relatively low species diversity but comparatively high endemism. The dominant reef-building corals of the TEP are the Pocillopora corals, a ubiquitous Indo-Pacific genus commonly regarded as inferior reef-builder. In addition to being the dominant reef-builders in the TEP, the Pocilloporids have undergone a reproductive shift from internally brooding larvae through most of their Indo-Pacific range to free-spawning in the TEP. Using genetic data from the internally transcribed spacer (ITS) regions of the nuclear ribosomal DNA gene cluster, we show here that this apparent reproductive shift coincides with interspecific hybridization among TEP Pocillopora species. We document a pattern of one-way gene flow into the main TEP reef builder P. damicornis from one or both of its TEP congeners —P. eydouxi and P. elegans. Our data provide preliminary evidence that trans-Pacific gene flow in P. damicornis between the Central and Eastern Pacific is restricted as well (ΦST = 0.419, P < 0.0001). In combination, these results suggest that Eastern Pacific corals exist in relative isolation from their Central Pacific counterparts and interact with each other differently via hybridization.