Abstract <p>The high-latitude hotspots of freshwater fish diversity are of particular scientific value. Among salmonids, the assemblage of endemic charrs from the landlocked Kronotskoe–Uzon water system is one of the most diverse worldwide. In this study, we analyzed the variability of mitochondrial DNA haplotypes and microsatellite DNA loci in all described ecomorphs to gain insight into the evolutionary specifics of this assemblage. We found that ten sympatric morphs from the Lake Kronotskoe basin are genetically differentiated from each other, with limited gene flow. Three derivatives of Lake Kronotskoe charrs populate small isolated peripheral waterbodies. The diversification of the assemblage progressed through significant demographic events specific to the morphs, which current numbers differing by a factor of ten. Microsatellite variability suggests the presence of four genetic lineages of Kronotskoe–Uzon charrs, that correspond well with the morphological and trophic-ecological differentiation of the assemblage. The rate of genetic specialization varies among lineages, with the piscivorous morphs demonstrating the most pronounced genetic differentiation.</p>