Most of the reef-building corals have pelagic larval duration and thus estimating the spatial range of larval dispersal is of great importance for conservation. Spatial autocorrelation analysis is a well-established technique to estimate spatial dispersal range and useful for deciding conservation units and sampling strategies for species with limited larval dispersal. While a few studies have examined spatial genetic structure of reef-building coral species using several loci and provided important insights on spatial genetic structure within coral population, no study has ever used genome wide loci and compared its result with dispersal range directly surveyed in the field. In this study, to examine the robustness of spatial autocorrelation method to estimate larval dispersal in coral species, we examined spatial genetic structure of reef-building coral species, Heliopora coerulea at two different reefs (Shiraho and Akashi) using a moderate number of genome-wide SNPs derived from MIG-seq analysis as well as 9 microsatellite loci for a comparison.