The article presents the results of comprehensive archaeological and paleobotanic research in the settlement Tytkesken-2 (Gorny Altai). In Tytkesken-2 settlement layers containing artifacts are separated by layers of sand of aeolian origin. Due to this we have a relative chronology for the eight cultural horizons on the length of time interval from the Late Mesolithic to the Chalcolithic period. Stratigraphic observations are complemented with the radiocarbon data, obtained for the three horizons of the Neolithic age. This allows us to give absolute and calendar dating of individual complexes and build periodization Mesolithic-Chalcolithic cultures of the Middle Katun. The territory of settlement was covered by forests in the Neolithic period. Forest became a barrier, contributing to the formation of eolian sediment in the Neolithic period, which is recorded at the beginning of the soil profile. In the final Neolithic era (srednekatunskaya culture) forests in this area were preserved for some time. In the Calcolithic and Bronze age forests were reduced and replaced by steppe communities. The populations of Tytkesken-2 settlement from the Mesolithic to the Chalcolithic ages were mainly engaged in ungulate animals hunting. The houses did not burn, people left the place voluntarily due to changes in the resource base or climate conditions.