Precious corals belong to family Coralliidae (Anthozoa: Octocorallia) are economically and biologically important taxa inhabited in the deep sea, although these corals are recently highly threatened by over-exploitation. To effectively conserve precious coral species, identifying species boundaries is primely important. In addition, examining genetic population structures is also crucial because coral populations are mutually connected via larval dispersal. Recently, the species status of Pleurocorallium konojoi and P. elatius has been doubted because traditional genetic markers could not discriminate the two species. In addition, no meta-population structure of precious corals (Corallium japanicum, P. konojoi and P. elatius) in Japan has been estimated due to the lack of valid genetic markers. To tackle these issues, we applied a genome-wide SNP analysis called as MIG-seq and first demonstrated P. konojoi and P. elatius are genetically different species. Secondly, we examined spatial genetic structure of C. japanicum to estimate the spatial extent of larval and gamete dispersal of C. japanicum in Kochi area. We found significant spatial genetic structure of C. japonicum up to 11 km, implying over-harvesting within this spatial range increase the risk of local extinction in Kochi.