The genetic parameters of donor and artificial populations of Siberian salmon (Oncorhynchus keta) have been analyzed. The parameters were obtained with the use of different molecular markers as well as mathematic modeling based on experimental data. The difference between results is explained by the different resolving power of individual markers and/or stochastic effects. It is assumed that these factors together with temporal differentiation of spawning salmonid populations and the stable interpopulation gene flow constrain resolution of methods based on the use of molecular markers and designated for the analysis of differentiation of salmonid populations.