Species delimitation of corals is one of the most fundamental issues in coral reef ecology and biology. While morphological classification of closely-related coral species is often challenging due to the lack of characteristic features and high phenotypic plasticity, recent advances in molecular tools have revealed a number of cryptic lineages and species of corals. Most of these studies, however, examined only geographically limited areas. In the case of the blue coral Heliopora, there are currently two valid species (H. coerulea and H. hiberniana) as evidenced by integrated genetic and morphological analyses in Northwestern Australia. There are also two distinct genetic lineages of H. coerulea in the Kuroshio Current region which are morphologically and reproductively different from each other. Sampling from across the Indo-Pacific is essential for a more complete picture of speciation and phylogeographic patterns. Here, to unveil phylogenetic relationship and speciation patterns of the genus Heliopora, we applied Multiplexed ISSR Genotyping by sequencing (MIG-seq) method for >1,000 colonies of Heliopora across the Indo-West Pacific.