Abstract The narrow-clawed crayfish Pontastacus leptodactylus is a large native European astacid crayfish species distributed in the drainage area of the Azov, Black and Caspian Seas. The species shows immense morphological diversity across its range. Various species and subspecies have been described and, recently, eight species and two subspecies were confirmed in the updated classification of freshwater crayfishes. However, genetic diversity studies of the species are scarce, mostly from limited geographical areas. Therefore, we aimed to analyse the genetic diversity of this species using mtDNA and nuDNA from across their distributional range to verify the presence of described species. Analyses of individuals from 65 populations and 14 countries confirmed the existence of three divergent mtDNA phylogroups corresponding to the geographical area of Central and Southern Europe, Eastern Europe and Asia, and Turkey. Analysis of ancestral ranges revealed the Black Sea basin as the most likely area of origin. The nuDNA analysis showed low diversity partially corresponding to the mtDNA pattern. All analyses showed mitonuclear discordance indicating the existence of a single species. Therefore, we point out the possibility of taxonomic inaccuracy with the current number of valid species within the P. leptodactylus species complex.