The relationships of the stone charr Salvelinus malma kuznetzovi, an endemic taxon to the Kamchatka River basin, were inferred from analysis of the nucleotide sequences of the mitochondrial DNA control region ( CR ) and cytochrome b ( Cytb ) and cytochrome oxidase-1 ( COI ) genes, as well as the nuclear lactate dehydrogenase gene ( LDH-C1 ). Genealogical analysis of mtDNA haplotypes confirmed the phylogenetic closeness of S. m. kuznetzovi, S. albus, and S. m. malma and showed that the above taxa represent the Beringian phylogenetic group of charr. The level of mtDNA divergence between S. m. kuznetzovi, S. albus, and S. m. malma did not exceed the intraspecific variation in Northern Dolly Varden populations. The existence of a cryptic Pleistocene refugium in the Kamchatka River basin has been substantiated; nevertheless, extensive and complex studies of charr of the Beringian group are needed.