The genetic structure of Salmo dentex and its phylogenetic relations to sympatric salmonids in the Neretva and Skadar River basins were evaluated using mitochondrial DNA (mtDNA) control region, eight microsatellites, and somatolactin (SL) gene. In the Neretva River basin of Bosnia-Herzegovina, the results based on mtDNA analysis showed extensive haplotype sharing between S. marmoratus, S. dentex, and S. trutta, and were therefore not conclusive; however, F-statistics and assignment testing based on nuclear DNA markers indicated that S. dentex of the Neretva basin were grouped in a genetically unified cluster with S. marmoratus in the Neretva basin. Using the same analytical approach, S. dentex from the Skadar basin in Montenegro appeared to be genetically distinct from S. marmoratus in the same basin and indistinct from local S. trutta. Molecular data also indicated that S. dentex of the Neretva basin in Bosnia-Herzegovina are not closely related to S. dentex of the Skadar basin in Montenegro. Based on these results, we hypothesize S. dentex to be a particular life history form of S. marmoratus in the Neretva basin and of S. trutta in the Skadar basin. These results clearly demonstrate that S. dentex does not represent a monophyletic lineage and should not be considered a distinct species.