Based on the morphology and size of chitin, we have identified the Gyrodactylus sp. that infected Carassius auratus gibelio Bloch, Abramis brama orientalis Berg, Gymnocephalus cernua Linnaeus, and Oncorhynchus mykiss Walbaum from the Ergis River are G. sprostonae, G. elegans, G. prostate, and G. brachymystacis, respectively. The comparison of the internal transcribed spacer (ITS) sequences of Gyrodactylus sp. with the data in GenBank indicated that the homology of the four Gyrodactylus sp. species with the GenBank data are all higher than 99.3%, which are consistent with morphological results. Phylogenetic analysis revealed that G. brachymystacis and G. sprostonae belong to one branch of the subgenus G. Limnonephrotus, while G. elegans and G. prostate belong to one branch of the subgenus G. Gyrodactylus, and these two subgenera have very low genetic relationship.