Comparative mitogenomes provide new insights into phylogeny and taxonomy of the subfamily Xenocyprinae (Cypriniformes: Cyprinidae).

is a cyprinid subfamily that not only has a discrete geographic distribution but also has a long history dating to the Early Miocene. However, it is controversial whether systematic classification and some species validity of exist, as well as its phylogenetic relationships and evolutionary history. In the present study, we first reviewed the description and taxonomic history of , and then the complete mitochondrial genome of , an endemic and locally distributed species belonging to , was sequenced and annotated. Finally, all the mitogenomes of were compared to reconstruct the phylogenetic relationship and estimate the divergence time. The results showed that the mitogenomes are similar in organization and structure with 16618-16630 bp length from 12 mitogenomes of eight species. Phylogenetic analysis confirmed the monology of and illustrated three clades within the to consist of ambiguous generic classification. is a valid genus located at the base of the phylogenetic tree. The genus was originally monophyletic, but was excluded. Divergence time estimation revealed that the earliest divergence within occurred approximately 12.1 Mya when separated from the primitive s. The main two clades ( and ( + + )) diverged 10.0 Mya. The major divergence of species possibly occurred in the Middle to Late Miocene and Late Pliocene, suggesting that speciation and diversifications could be attributed to the Asian monsoon climate. This study clarifies some controversial issues of systematics and provides essential information on the taxonomy and phylogeny of the subfamily .