Pipistrelles of the genus Hypsugo are among the rarest bats in Japan, known from a handful of records. In June 2018, a sequence of echolocation calls apparently by a bat of this genus was recorded by an automatic ultrasound recorder on the island of Okinawa. The calls closely resemble H. pulveratus, a Chinese species never before recorded in Japan, and H. alaschanicus, a very rare species in Japan. They also resemble calls of Hypsugo sp. bats from a small population recently discovered on nearby Amami-Oshima Island. The extreme rarity in our recordings, combined with lack of detection in Okinawa by other surveys, suggests that the individual was a vagrant. However, given the cryptic nature of the species on Amami, it remains possible that there is a small and likely endangered resident population, underlining the need for further bat surveys on Okinawa and other Nansei Islands.