Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex includes four recognized species and four main color morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a noncongruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish. (1) the current distribution range of species reflects their mode of diversification and (2) the gene tree is congruent with the species tree as substantiated by multiple independent molecular markers.In addition, environmental characteristics, life-history traits, and biological interactions gained from field observations and experiments can inform the processes that drive diversification.In the context of understanding speciation mechanisms, as described above, marine systems challenge conventional allopatric speciation. The paucity of physical barriers combined with the potential for long-range dispersal of early life-history stages makes the study of speciation in marine organisms a unique 1 2 1 8