<p>Charrs of the genus <i>Salvelinus</i> (Salmonidae) have a modern Holarctic distribution and provide an interesting model for research into intercontinental exchanges. Here, we focus on the Arctic phylogenetic lineage, whose range is disjunct between two continents. Herein, combined sequence data from both the mitochondrial (cytochrome <i>b</i>, cytochrome <i>c</i> oxidase-<i>1</i>, and control region) and nuclear (growth hormone gene 2) markers were used to test the alternative hypotheses on the origin of Palearctic and Nearctic charrs of the Arctic lineage and their relationships. Three independent lineages were identified: the Arctic lineage of <i>Salvelinus taranetzi</i>, the Atlantic lineage of <i>Salvelinus alpinus</i>, and the Beringian lineage of <i>Salvelinus malma malma</i>. The maximum genetic distance within each lineage did not exceed the minimum genetic distance between the lineages. Close relatedness between Palearctic and Nearctic charrs of the Arctic lineage has been confirmed by our analyses of the mitochondrial and nuclear markers. Signals of historical hybridization were detected between the Arctic and Atlantic lineages and within the Arctic lineage in northeastern Asia. Our results clearly show that the polytypic species <i>Salvelinus alpinus</i> complex includes two species (<i>S. alpinus</i> and <i>S. taranetzi</i>) with modern limited ranges, which is an alternative to the generally accepted concept.</p>