Here we describe the biological and ecological differences between partially anadromous Dolly Varden and riverine stone charr distributed in the Kamchatka River middle course. Endemic stone charr, being the ambush predator, is defined by the accelerated growth and prolonged lifespan, robust body and large mouth, as well as specific marble colouration since an early age. The significant restriction in gene flow between the stone charr and benthos-eating Dolly Varden was supported by an allelic distribution of eight microsatellite loci. Herewith, the identity of mitochondrial DNA control region and intron sequences of growth hormone and metallothionine genes confirms a relatively recent diversification of the groups within the single basin. We suggest the key role of the specific environment for reproduction isolation of stone charr. It occupies coniferous taiga zone with dark-coloured water, whereas Dolly Varden spawns uppercourse in the zone of stunted, windblown forest. Conifer litter decomposition products could drive natural selection of stone charr via metabolism acceleration and resistance to toxicants. The metabolic difference could promote piscivory and development of the specific morphological peculiarities of the stone charr. Therefore, we present the first evidence in favour of trophic-based sympatric diversification in a river basin at high latitudes.