Background. Precious corals, coralliid corals (Anthozoa: Octocorallia), play an important role in increasing the biodiversity in the deep sea. Currently, these corals are highly threatened because of overfishing due to increased demand together with elevated price. Deep sea precious corals Pleurocorallium elatius and Pleurocorallium konojoi are co-distributed in Japanese waters and have distinct morphological features (1) terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status for considering their conservation. Methodology. We collected a total of 87 P. elatius and P. konojoi around from Ryukyu Islands to Shikoku Island, geographically separated by approximately 1300 km. We used multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared. Results. Pleurocorallium elatius and P. konojoi share a same mtDNA haplotype as has been previously reported however, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs. Conclusions. This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of conservation of these two species, especially P. elatius, whose population has been dramatically depleted in the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for delimiting closely related octocoral species that were indistinguishable using traditional genetic markers (mtDNA and EF).