We describe a new sea spider species, Pantopipetta hosodai sp. nov., based on one juvenile female collected from a submarine cave (‘Akumanoyakata’ Cave) in Shimojijima Island, Miyako Island Group, Ryukyu Islands, southwestern Japan. It was collected from the second slope zone of the cave, 80–100 m from the entrance, no light, low salinity and with rocky substrate. This is the first record globally of a Pantopipetta species from a submarine cave and anchialine environment. Pantopipetta hosodai sp. nov. resembles Pantopipetta auxiliata, Pantopipetta lenis and Pantopipetta oculata in having auxiliary claws, but differs from them in having a palp with three short distal articles, lateral processes without dorsodistal tubercles, coxae 1 and 3 of legs 1–3 each with one long dorsal tubercle and one dorsodistal tubercle bearing a seta on each femur. Features of the palp appear to delineate two species groups in Pantopipetta, i.e. (1) those having four small distal articles, and a small, basal palp article between the lateral cephalon process and longest palp article (eight-articulate palp) and (2) those having three small distal articles, and lacking the small basal article (six-articulate palp), but further detail examination of the described species is needed. We discuss the diagnostic characters separating Pantopipetta and Austrodecus and the generic affiliation of Austrodecus aconae. Few pycnogonids from marine or anchialine caves have been identified to species, and it is generally unknown whether cave-dwelling pycnogonids tend to be troglobites.