Sea urchins have a wide variety of symbionts on their body surfaces and inside their bodies. Copepods of the genus Clavisodalis (Taeniacanthidae) collected from the esophagus of sea urchins of the genera Diadema and Echinothrix in southern Japan were identified based on their morphological characteristics, and molecular analysis was conducted to determine whether genetic variation occurs in copepods from different localities and hosts. Morphological observations identified individuals from southern Japan as Clavisodalis sentifer Dojiri and Humes, 1982, making this the first record of this species in the northern hemisphere and the first record of its genus in Japan. Morphological and molecular analysis suggested that the copepod specimens collected from multiple hosts across two genera would be the same species. Considering the typically observed high level of host specificity among taeniacanthid copepods, the utilization of hosts from two genera by C. sentifer is noteworthy.