Kuznetsk Alatau is located in the Sayan montane conifer forests ecoregion. This ecoregion covers the middle-elevations of the highest mountains in the Altai-Sayan mountain range of central Asia. It lies between the Siberian taiga to the north, and the Mongolian steppe to the south. The ecoregion is characterized by mountains desiccated with river valleys, high levels of precipitation, and high biodiversity. Flora is generally dependent on the elevation and terrain, with forest having three main subzones based on altitude: light needle-leaf sparse taiga, dark needle-leaf taiga, and dark taiga.