In this study we describe one new species of Dactylogyrus Diesing, 1850 and three new species of Bivaginogyrus Gussev and Gerasev in Gussev, 1985 (Monogenea: Dactylogyridae) from two freshwater fishes Gnathopogon elongatus elongatus (Temminck and Schlegel, 1846) and G. caerulescens (Sauvage, 1883) (Cypriniformes: Gobionidae) endemic to Japan. Further, G. elongatus is a new host record for Paradiplozoon skrjabini Achmerov, 1974 (Monogenea: Diplozoidae). Dactylogyrus tamoroko n. sp. is most similar to D. chenjiagengi Zhang in Zhang, Zhou, and Wen, 1990, D. clypeatus Gussev, 1955, and D. gnathopogonis Yamaguti, 1963; it differs from these three congeners by the bifurcate base of the accessory piece. Bivaginogyrus japonicus n. sp. is close to D. polylepidis Alvarez Pellitero, Simon Vicente, and Gonzalez Lanza, 1981, but it can be separated from the latter species based on its uniform-sized marginal hooks. The new species was connected to the cartilage tissue of the gill using filament-like structures, which are assumed to be derived from secretions of the reservoirs associated with each marginal hook. Bivaginogyrus cingulatus n. sp. resembles D. navicularis Gussev, 1955, D. trullaeformis Gussev, 1955, and D. imberbis Wu and Wang, 1983, but the new species is distinguished from these three species by having its inconspicuous outer roots. Bivaginogyrus exiguus n. sp. is comparable to D. pandus Wu and Wang, 1983 and D. colpodes Wu, Wang, and Song, 1983, but differs from these two species in having a shorter penis. Molecular phylogenetic analysis indicates that Bivaginogyrus is a paraphyletic group and shows affinity to “Dactylogyrus” species parasitic on gobionid fishes. However, most of those closely related Dactylogyrus species are yet to be described for their internal morphology and should accordingly be redescribed. The three new species of Bivaginogyrus are assumed to have been co-introduced along with G. e. elongatus into non-native regions of this host.