Fish species of the genus Capoeta are known for their special mouth morphology (inferior mouth with the horny edge to the lower jaw), short dorsal fin with seven to nine branched rays, and their tumultuous taxonomic history. The genus Capoeta has had a complex evolutionary history with high diversification in the Middle East and is closely related with genus Luciobarbus. Earlier attempts to clarify the complex taxonomy of the group established four species groups, namely C. capoeta, C. damascina, C. tinca, and C. trutta species group. Based on this study, the C. capoeta group currently includes nine taxa (seven previous + two newly included members) and all reviewed in this paper based on morphological characters and mitochondrial genes. Capoeta macrolepis, revalidated as a distinct species, and Capoeta fusca are additional members of the C. capoeta group. Molecular time tree shows that the separation of Capoeta from its relative Luciobarbus was about 12.43-16.99 MYA. Based on the time tree presented herein, the high diversity of Capoeta in the Tigris-Euphrates system, the nesting of Capoeta within the tetraploid Luciobarbus in the mitochondrial trees and the high diversity of Luciobarbus in the Tigris-Euphrates system, it is proposed that the origination and diversification of Capoeta occurred in the palaeo-drainages of the Tigris-Euphrates system. From here, dispersion of Capoeta to the other nearby basins could have been possible through freshwater corridors during the Pliocene or Pleistocene.