We have studied on the population structure of whitefish, Coregonus lavaretus pidschian, from the waterbodies situated in the upstream of the Ob’ and Yenisei Rivers. It has revealed significant differences among most of the whitefish populations in the meristic characters. The number of gill rakers on the first branchial arch and the number of perforated scales in the lateral line can significantly differ between neighbor populations. It is suggested that the number of perforated scales in the lateral line can consider as the character close to the evolutional neutral one.