Background. The purpose of this work was studying of interaction between morphologically similar forms of the pidcshian-like whitefishes inhabiting restricted territory of “riverine-lacustrine” system situated in the Bolshoi Abakan Rriver basin. Material and methods. In the morphological analysis were used 141 whitefish individuals from Lake Karakul and 26 - from the Bolshoi Abakan River. In the genetic analysis 11 and 26 whitefish individuals were used respectively. For them the sequences of a gene 16S-ND1 of mitochondrial DNA (mtDNA) and ITS1 of nuclear DNA (nDNA) were defined. Results. The whitefish populations clear differ on the gill raker numbers on the first branchial arch, growth. The analysis of the 16S-ND1 mtDNA genes variability revealed among them several divergent lineages and two lineages were revealed on the structure of ITS1 fragment of the nDNA. Conclusions. Based on the obtained data it is proved that two genetically divergent populations of the morphologically same forms of pidcshian-like whitefishes inhabiting the “riverine-lacustrine” system (the Bolshoi Abakan River - Lake Karakul). Our results are supported a hypothesis of multiple hybridization between week differentiated populations/form of pidcshian-like whitefishes inhabiting region during the postglacial period.