Abstract: Partial sequences of mitochondrial gene were obtained by PCR amplification from 5 species in genus Pseudecheneis recorded in China and out group species Bagarius yarrelli and Glyptothorax fukiensis honghensis. The results of sequence analysis showed that there was no difference in partial Cyt b sequences between Pseudecheneis intermedius and P. paviei that constituted a haplotype. This result supported that P. intermedius was the synonym of P. paviei. Molecular trees of NJ, MP and ML were individually constructed based on the partial Cyt b sequences. The structure of the three types of molecular trees was basically consistent, indicating that the genus Pseudecheneis was a monophyletic group. The samples of P. sulcatus respectively got from Nujiang River and Irrawaddy River valleys could be clustered individually, whereas the samples got from different river valleys could not be clustered together. Samples of other species could be clustered respectively. The results implied that the taxonomic status of P. sulcatus between the Nujiang and the Irrawaddy basins deserved to further study in the future.