Previous studies have shown that Acrossocheilus paradoxus from Taiwan and A. wuyiensis from Minjiang River are closely related species, and they are difficult to distinguish in morphological characteristics. Therefore, the validity of the two species is still controversial. In the present study, completemitochondrial COⅠ gene sequences were used to investigate the species validity of A. paradoxus and A. wuyiensis. A total of 21 haplotypes were obtained from 76 samples of 6 species in the genus. Phylogenetic trees constructed by maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) methods showed that the two species formed a monophyletic group. Genetic distance analysis showed that the average Kimura 2-parameter distance between A. paradoxu s and A.wuyiensis was only 0.853%, far less than the 2% genetic distance threshold of DNA barcode among species. The ASAP method we also used to build species partitions, the result shows the two species were classified as the same species. Therefore, A.wuyiensis distributed in Minjiang River and A. paradoxus distributed in Taiwan should be a same species, and A.wuyiensis is the synonym of A. paradoxus.