The genetic discrimination of two species of the genus Capoeta, C. tinca (Heckel, 1843) and C. banarescui Turan et al., 2006, which is represented by many endemic species in Anatolian Turkey, has been investigated by analysing the partial 16S ribosomal DNA gene (525 bp). A total of 85 fish was sampled from two localities in the Marmara basin and 5 localities in the Black Sea basin. The amount of 16S rDNA sequence divergence separating these two taxa (mean 1.19%) is within the range observed for 16S rDNA variation between other species of freshwater fishes. The derived haplotypes (h: 28) were strictly local and were not shared between species or populations within species. Three types of phylogenetic tree (Bayesian, MP and ML) clearly showed C. banarescui and C. tinca as distinct species separated with significant bootstrap values (BI:94, MP:88, ML:8 I), confirming previous conclusions based on morphometric and meristic characters. Furthermore, four novel SNPs were identified, allowing discrimination between two species. AMOVA tests revealed that populations of Capoeta in Northeastern Anatolia can be divided into two main groups: Coruh River group, including SVS, TRT and ISP populations, and Yesilirmak-Harsit group, consisting of ALC and HRS populations. These results indicate the effectiveness of mitochondrial 16S rDNA gene sequences for both species identification and the phylogenetic analysis of Capoeta species.