The coral reef ecosystems in the Indo-Pacific Ocean harbor high biodiversity. This high diversity of reef-building corals, the foundation of biodiversity, could be originated from physical segregation of populations (allopatric speciation) and various types of ecological speciation, although the speciation patterns of coral species are not well-understood. Here, we examined genome-wide SNPs data of the blue coral, Heliopora spp. to reveal its speciation patterns. We collected in total 844 samples of Heliopora spp. from the Indo-Pacific; 46 sites along Kuroshio-Current and 8 sites in Western Australia. Clustering analysis revealed three different genetic lineages (type-A, A’ and B) in the Kuroshio region and two additional genetic lineages (Heliopora coerulea and H. hiberniana sp. nov.) in Western Australia, suggesting possible allopatric speciation among geographically separated populations. Gonadal observation of a total of 468 samples in the Kuroshio region (A, A’ and B), revealed different reproductive timing causes reproductive isolation between the different lineages even in sympatric habitats. Fixed substitution in the biological clock related genes that control reproductive timing was found between A(A’) and B in the Kuroshio region, implying allochronic reproductive isolation. These data imply both allopatric and allochronic speciation occurred in the blue coral.