The ophiuroid species listed were collected by benthic faunal surveys from 2016 to 2018 in submarine caves of the Ryukyu Islands, southwestern Japan. The material includes 20 species from 8 families, Amphiuridae, Ophiocomidae, Ophiodermatidae, Ophiolepididae, Ophioleucidae, Ophiomyxidae, Ophionereididae and Ophiotrichidae. This is the first comprehensive report of submarine cave-dwelling ophiuroids from Japanese waters. Also provided is a redescription of a rare species, Dougaloplus echinatus (Ljungman, 1867), with a detailed description of its ossicle morphology. The species has previously been reported from Brazil, Australia, Eastern Indian Ocean to Southern China, in 11–118 m depth, and this is the first record of D. echinatus from Japanese waters. A brief discussion of the scarcity of submarine cave systems, and the need for their conservation, is provided.