In this study, the phylogenetic and phylogeographic relationships among Cyprinion macrostomus HECKEL, 1843, Cyprinion kais HECKEL, 1843 and Carasobarbus chantrei SAUVAGE, 1882 samples from Anatolia were analysed. While doing this, mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Nuclear DNA inter-simple sequence repeat (ISSR) were used. PCR amplified the complete mtDNA NADH 3/4 dehydrogenase (ND-3/4) gene. Amplified fragment was digested by 14 restriction enzymes that produced 14 composite haplotypes for these populations. All identified mtDNA haplotypes differed from each other having a specific genetic profile. The genetic diversity among the mtDNA haplotypes of C. macrostomus, C. kais, and C. chantrei populations from drainage basins of the Mediterranean and those from the drainage basin of the Persian Gulf was purported by the extrapolation of mtDNA PCR-RFLP data. This result is also supported by the data explaining the geological history of Anatolia. Broadly, the data from mtDNA and from nDNA was consistent.