ABSTRACT: While the center of the world’s marine biodiversity is undoubtedly the central West Pacific, the mechanisms by which such high biodiversity was generated and perpetuated are still under debate. In this study, we amplified both a mitochondrial DNA control region and 4 microsatellite loci to elucidate the historical phylogeography of the neon damselfish Pomacentrus coelestis in the West Pacific and used the distribution of alleles to test the ‘Center of Origin’ hypothesis. Two deeply divergent clades (‘Pacific’ and ‘Micronesia’) were identified, and the results of hierarchical analysis of molecular variance (proportion of variations among regions, Φ_CT = 0.752, p < 0.01) and Bayesian assignments of genotypic data suggest a major genetic break between these clades. Demographic parameters, Tajima’s D and Fu’s Fs values, also indicate that these 2 lineages have different historical trajectories, indicative of the existence of more than 1 species within the complex currently assigned to P. coelestis. To avoid misinterpretation of past dispersal inferences, these 2 lineages were analyzed separately, and the Pacific clade was found to lack a distinct dispersal direction, probably due to rapid population expansion in the past. In contrast, the Micronesian clade showed a northeastwardly cladogenesis. Additionally, mixed lineages were found in the Raja Ampat Islands, suggesting that the Micronesian clade fits not only with the prediction of the Center of Origin hypothesis, but also the ‘Center of Overlap’ hypothesis. Our results suggest that multiple evolutionary processes may have acted on single species, either simultaneously or at different times, and have important implications for reef fish management in the West Pacific.