We review the genus Anacaena Thomson, 1859 from the Ryukyu Archipelago, southern Japan. Three aquatic species are recognised: A. torikaiisp. nov. from Amami-ôshima Island, A. okinawanasp. nov. from Okinawa-jima Island and Kerama Islands, and A. kumejimanasp. nov. from Kumejima Island. All three species are very similar, with the morphology of the aedeagus being essential for a reliable identification. Dorsal colouration is also useful as a diagnostic character, despite some variation within species. We observe a possible geography-based variation between A. okinawana from Okinawa-jima I. and the neighbouring Kerama Is., but we treat both populations as conspecific based on genital morphology. Anacaena kumejimana and A. okinawana share many morphological characters possibly indicating their close relationship. We compare the endemism of aquatic Hydrophilidae in the Ryukyu Archipelago to that in other groups of aquatic beetles: the proportion of endemic species is higher in aquatic Hydrophilidae than in Dytiscidae, but much lower than in stream-inhabiting Hydraenidae and Elmidae. A list of Japanese species of Anacaena and a key to the Japanese species of the genus are provided.