The molecular phylogeny of the Anatolian species of the genusChondrostoma(Cypriniformes: Leuciscidae) was studied by sequencing of the mitochondrial cyt b gene. A total of 144 tissue samples from 14 described species were collected from 35 different localities in Turkey. In total, 74 cyt b haplotypes were identified. Haplotype network construction and phylogenetic analysis allocated all 14 species to two main haplogroups that are congruent with those currently accepted on the basis of morphological characteristics. The first haplogroup, the Nasus lineage, is distributed across Caucasia and the Black Sea and Marmara regions and is also represented in the Aegean basin. The second haplogroup, the Regium lineage, is distributed from eastern Anatolia to the Mediterranean Sea basin. Based on estimates generated in this study, the radical divergence between the mainChondrostomahaplogroups in Turkey occurred during the late Miocene (Tortonian stage) and late Pliocene Period, approximately 5.82 Mya (8.48-3.45 Mya). The splitting of the Nasus lineage occurred approximately 5.11 Mya, in the early Pliocene, and the Regium Lineage diverged from its sister group, the Nasus lineage approximately 4.77 Mya. The primary diversification events for the species belonging to these two haplogroups occurred in the Late Pliocene to Early Pleistocene which coincides with the uplifting of the Anatolian plateau about 2.5-3.0 Mya.