We encountered two cases of infection with large female nematodes of the genus Philometra Costa, 1845 in the body cavity of a map puffer Arothron mappa (Lesson) caught off Okinawa, Japan, and a blackspotted puffer Arothron nigropunctatus (Bloch et Schneider) caught off Queensland, Australia, both reared in aquariums in Japan. No morphological difference was observed between the nematodes from A. mappa and A. nigropunctatus. We identified the nematodes as Philometra pellucida (Jägerskiöld, 1893) based on their morphology. The sequences of the nematodes from both hosts were identical to each other (1,643 bp) and formed a clade with other 17 nematodes belonging to the genera Philometra and Philometroides Yamaguti, 1935 with high bootstrap value (bp = 100). It is the first time that the genetic data on P. pellucida are provided. Philometra robusta Moravec, Möller et Heeger, 1992 is synonymised with the former species.