Uncovering Cryptic Coral Species in Japan’s Precious Coral Fishery: Conservation and Sustainable Management Implications

Accurate estimates of catch and trade volumes for target species are essential for effective resource management. In the precious coral fishery, lesser-known species may be unintentionally harvested in addition to major targets, due to identification based solely on color, ignoring biological species boundaries that are critical for sustainable use. In this study, we identified an unknown coral species, Pleurocorallium sp. 1, that was collected together with three major species commonly harvested in Japan ( Corallium japonicum , P. konojoi , and P. elatius ). Phylogenetic analysis based on three mitochondrial regions showed that P. sp. 1 forms a monophyletic group with P. secundum , which is primarily distributed in Hawaii. In contrast, a phylogenetic tree based on 4,077 SNPs from Multiplexed ISSR Genotyping by sequencing revealed that P. sp. 1 forms a clade distinct from P. secundum , suggesting that it may represent an undescribed species. To our knowledge, this is the first study to reveal that genetically distinct species beyond the three major ones are being harvested in Japan’s precious coral fishery. Surprisingly, our analysis also uncovered a novel cryptic lineage among samples identified using gross morphology, as P. konojoi called Pleurocorallium sp. 2. These findings highlight the need for genomic identification of harvested precious corals to ensure sustainable use and proper resource management. Future work should clarify the taxonomic status of P. sp. 1 and P. sp. 2 through detailed morphological assessments. It should also investigate their geographic distributions and abundance, and assess the extent to which these undescribed species have been harvested in commercial fisheries. • A cryptic species was collected together with Japan’s three major precious corals. • An undescribed species, morphologically resembling white coral, is genetically distinct. • Genetic tools are vital for sustainable management of precious coral fisheries.