A new species of the bitterling genus Acheilognathus, Acheilognathus changtingensis sp. nov., was recently discovered from Changting County in Hanjiang River, Fujian Province, Southeastern China. It can be diagnosed by the following combination of characters: dorsal fin with three simple and 15 (occasionally 14) branched fin rays, anal fin with three simple and 12 (occasionally 11) branched fin rays; dorsal fin pale and anal fin slightly pale; white spots on anal-fin rays forming a transverse band, and anal fin margined with white band in males. Its unique characters are the many dispersed black spots on the dorsal, anal, pelvic, caudal fins, and on the head. Using the mitochondrial cytochrome Jb gene as a molecular marker, we reconstructed phylogenetic trees of A. changtingensis sp. nov. and other species in Acheilognathus to confirm its taxonomic status and study its speciation. Analyses of both morphological and molecular data consistently indicated the taxonomic status of the present new species. The results also show that A. changtingensis sp. nov. and Acheilognathus macropterus are sister species that diverged about 14.50 MYA by geographical isolation.