The genus Rutilus is widespread in the western and central Palearctic region. In the Caspian Sea the taxonomic status of different populations of Rutilus lacustris has been debated due to different sub-specific names attributed to each population. In this project we considered populations of R. lacustris and Rutilus frisii from the southeast and southwest Caspian Sea and the Aras River in the Kura River drainage. We used a combination of genomic (genotyping-by-sequencing, GBS) and mitochondrial cytochrome c oxidase subunit I (COI) partial sequence data. Our aims were to: a) infer the relationships among the respective populations, and b) provide guidelines for conservation and management of R. lacustris in the southern Caspian Sea.