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The aims of this study were to testify a phylogenetic hypothesis for the genus Rutilus in the Southern Caspian Sea using sequence variation of mitochondrial and nuclear genes and to define the taxonomic status of phylogenetic clades represented in this region. Phylogenetic analysis was based on the variability of mitochondrial genes cytochrome b and cytochrome c oxidase subunit I and nuclear recombination activating gene 1 and inter-photoreceptor retinoidbinding protein. Compared to previous studies, this phylogenetic analysis included significant material from the South Caspian, both from the collected samples and from GenBank data. As a result, only two species of Rutilus were confirmed in the ichthyofauna of the studied region. The first of them corresponds to R. lacustris, therefore, materials from the South Caspian can be included in genetically identified vouchers of this species to determine its morphological diagnostic features. The second species represented separate sister phylogenetic lineage for the Pontic populations of R. frisii sensu lato. Due to the low genetic distance between the Caspian and Pontic lineages and the strong overlap of their morphological features, but previously proven divergence in separate Pleistocene refugia, the Caspian populations are classified in this study as a subspecies R. frisii kutum. [ABSTRACT FROM AUTHOR]