Traditionally, Capoeta populations from the southern Caspian Sea basin have been considered as Capoeta Capoeta gracilis. Study on the phylogenetic relationship of Capoeta species using mitochondrial cytochrome b gene sequences show that Capoeta population from the southern Caspian Sea basin is distinct species and receive well support (posterior probability of 100%). Based on the tree topologies obtained from Bayesian and Maximum Likelihood methods, three main groups for the studied Capoeta were detected: Clade I) Capoeta trutta group (the Mesopotamian Capoeta group) including closely related taxa (e.g. trutta, turani, barroisi) characterized by having numerous irregular black spots on the dorsal half of the body. This clade was the sister group to all other Capoeta species and its separation occurred very early in evolution possess, so we considered it as Old Evolutionary Group. Clade II) comprises highly diversified and widespread group, Capoeta damascina complex group (small scale Capoeta group), the Anatolian-Iranian group (e.g. banarescui, buhsei, damascina, saadii), characterized by small scales and plain body (absence of irregular black spots on the dorsal half of the body, except in some juveniles) with significantly later speciation event so called Young Evolutionary Group. Clade III) Capoeta Capoeta complex group (large scale Capoeta group, the Aralo-Caspian group) comprises very closely related taxa characterized by large scales and plain body (absence of irregular black spots on the dorsal half of the body) distributed in Aralo-Caspian water bodies (Capoeta, ekmekciae, heratensis, gracilis, sevangi) that has been recently diverged and could be considered as Very Young Evolutionary Group.