The boring sea urchin of the genus Echinostrephus (Echinometridae, Camarodonta, Echinoidea, Echinodermata) is composed of two species, namely, Echinostrephus aciculatus A. Agassiz, 1863, and Echinostrephus molaris (de Blainville, 1825). In Japan, E. aciculatus is distributed from Tateyama, Chiba Prefecture, to the Osumi Islands, Kagoshima Prefecture, whereas E. molaris is distributed from the Tokara Islands, Kagoshima Prefecture, and southwards. They can be distinguished by the color of spines and by the number of pore pairs in each row on ambulacral plates. Echinostrephus aciculatus has four pore pairs in each row on the aboral side, whereas E. molaris has only three pore pairs in each row across all the ambulacral plates. However, these spines are fragile, and they often break, making them an unreliable identification trait. Pore pairs also often show individual variation. Thus, re-examining these species based on molecular data is necessary. In this study, Echinostrephus spp. were collected from tropical waters (Okinawa and Ogasawara Islands) and subtropical waters (Shirahama, Wakayama Prefecture) within the Kuroshio Current basin, and molecular and morphological comparisons were conducted. Molecular phylogenetic analysis based on mitochondrial COI sequences showed that E. aciculatus and E. molaris formed a distinct clade, and E. molaris collected from Japan showed no regional variations, making Shirahama a northernmost record. Spine color and the number of pore pairs, especially at the first to third ambulacral plates from the aboral side, were confirmed to be valid taxonomic traits that clearly distinguish each species clade.
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