Gobionine species belonging to the generaPseudorasbora,Pseudopungtungia, andPungtungia(Teleostei; Cypriniformes; Cyprinidae) have been heavily studied because of problems on taxonomy, threats of extinction, invasion, and human health. Nucleotide sequences of three nuclear genes, that is, recombination activating protein gene 1 (rag1), recombination activating gene 2 (rag2), and early growth response 1 gene (egr1), fromPseudorasbora,Pseudopungtungia, andPungtungiaspecies residing in China, Japan, and Korea, were analyzed to elucidate their intergeneric and interspecific phylogenetic relationships. In the phylogenetic tree inferred from their multiple gene sequences,Pseudorasbora,PseudopungtungiaandPungtungiaspecies ramified into three phylogenetically distinct clades; the “tenuicorpa” clade composed ofPseudopungtungia tenuicorpa, the “parva” clade composed of allPseudorasboraspecies/subspecies, and the “herzi” clade composed ofPseudopungtungia nigra, andPungtungia herzi. The genusPseudorasborawas recovered as monophyletic, while the genusPseudopungtungiawas recovered as polyphyletic. Our phylogenetic result implies the unstable taxonomic status of the genusPseudopungtungia.