The mitochondrial cytochrome b gene was sequenced from Acantholingua ohridana from Lake Ohrid, Macedonia, and Salmo salar; and these sequences were compared to those previously obtained from S. trutta and five other salmonid species. In addition, a nuclear sequence, the first internal transcribed spacer (ITS1) of the ribosomal DNA, was obtained from A. ohridana, S. salar, and S. trutta and compared with sequences obtained from the same five salmonid species. Combination of these data with nuclear GH2C intron sequences for the same taxa yielded a combined dataset of approximately 2100 aligned bp for eight species. Phylogenetic analysis of all datasets supported the inclusion of A. ohridana in Salmo and a sister relationship between A. oridana and S. trutta.