Abstract: Taxonomy and phylogeny of the genus Abbottina fishes in the subfamily Gobioninae (Cypriniformes: Cyprinidae) remain unresolved. The current study utilized mitochondrial gene (cytochrome b) and nuclear loci (RAG1, MLH3 and MSH6) as molecular markers to reconstruct phylogenetic relationships of Abbottina fishes, and revised their classification by merging morphological evidence. The results showed that Abbottina rivularis and A. obtusirostris were monophyletic species. Abbottina lalinensis and A. liaoningensis were paraphyletic species, which formed a monophyletic group. Abbottina lalinensis+A. liaoningensis were nested within Microphysogobio fishes, and Abbottina obtusirostris was nested within Platysmacheilus fishes. Abbottina lalinensis+A. liaoningensis+A. obtusirostris+Platysmacheilus+Huigobio+Microphysogobio+Biwia fishes formed a monophyletic group, which were a sister taxon of Abbottina rivularis. Meristic and morphometric characters did not separate Abbottina lalinensis from A. liaoningensis. The molecular evidence and morphological evidence demonstrated that the genus Abbottina fishes include Abbottina rivulari and A. binhi (un-sampling in this study), and that Abbottina liaoningensis was a junior synonym of A. lalinensis, which needs further revision; and Abbottina obtusirostris was revised as Platysmacheilus obtusirostris.