In the present study, the mitochondrial COI sequences were sequenced for 43 unionid individuals, belonging to 13 species from 7 genera. Sequences were analyzed using Sequencer 4.05 software. Genetic distances were calculated using the Kimura 2-parameter model. The average intraspecfic distance found was 0.02623, much lower than the average interspecfic distance, which was 0.18472. The interspecfic distance between Anodonta woodiana elliptica and Anodonta woodiana pacifica was only a little higher than the intraspecific distance. This suggests that Anodonta woodiana elliptica and Anodonta woodiana pacifica are not separable as either subspecies or species. A molecular phylogeny of the Chinese freshwater unionidae was constructed based on mitochondrial COI sequences. The phylogenetic trees were constructed by the minimum evolution (ME) method, in which the 13 species were divided into three groups. The first group comprised Solenaia oleivora, Solenaia carinatus, Solenaia rivularis and Lamprotula caveata. The second group included Anodonta arcaeformis, Anodonta woodiana elliptica and Anodonta woodiana pacifica. While Lanceolaria gladiola, Lanceolaria grayana, Unio douglasiae, Lamprotula tortuosa, Acuticosta chinensis and Cuneopsis heudei made up the third group. Phylogenetic analysis of the genus Solenaia shows that the Chinese endemic species Solenaia comprise not three species as previously supposed, but four species, one of which has not yet been formally brought forward and described. COI sequences can provide useful information for phylogenetic studies in the Unionidae, and has important implications for these animals' conservation, especially for those considered to be endangered.