Little is known about where anguilliform fishes complete metamorphosis from the leptocephalus to juvenile stage. Conger myriaster leptocephali in the final stages of metamorphosing were collected from the estuarine portions of the lower Rokkaku River and in the northwest region of Ariake Bay. Three metamorphosing leptocephali with PAM/TM ratios of 0.27-0.34 were collected in the lower river, and five (PAM/TM, 0.30-0.46) were collected at sea stations in the bay. The collection of metamorphosing larvae of this species in a river estuary with lower salinity and high turbidity raises the question of how much these habitats are used by the metamorphosing larvae of this marine eel species.