The Markakol Reserve was organized in 1976 and is located on the territory of Markakol district. The area of 71,367 hectares, including 5,521 hectares — forested, 2,194 hectares are occupied by hayfields and 43,950 hectares — reservoirs.

The Markakol Nature Reserve is located in a mountainous area, at an altitude of up to 3,700 m above sea level and occupies most of Markakol Lake, located at an altitude of 1,495 m above sea level in the intermountain depression between Kurchumsky and Azutau ridges. The maximum depth of the lake is 23.8 m. 27 small rivers and streams flow into the lake: Baibaksu, Matabai, Urunhaika, Karabulak, Topolevka, Verkhnyaya Yelovka, etc.

The soil cover is diverse, there are mountain-tundra, mountain-forest, mountain-meadow, dark gray weakly podzolic, forest black-earthy, mountain forest-meadow, meadow-steppe and chernozem mountain-steppe leached, as well as meadow-chernozem, name-meadow, meadow-swamp, swamp and others soils.

The Markakol Nature Reserve is located in three different climatic zones: extremely continental Mongolian, continental Western Siberian. Southern Altai belongs to the Altai-Saurtarbagatai climatic region.

The vegetation cover is interesting and diverse. There are stony and moss-shrub (thorn) tundras, deciduous woodlands, alpine and subalpine meadows, kobresia, light coniferous taiga with an admixture of dark coniferous species, larch forest-steppe, grass-grass steppes, floodplain sedge meadows, swamps, etc.

19 types of forests are identified, the most widespread are larch forests (rocky, subalpine, fir-moss, fir-mixed grass, currant, meadowsweet, grass-mixed grass, etc.), fir trees and spruce forests growing in the southern part of the mountain taiga belt (1900-2100 m above sea level) are less common, for example, grass-mixed and broad-grass fir trees, etc., as well as birch forests (mixed grass, reedgrass, sedg-marsh), aspen, poplar, willow, etc. In the undergrowth of the Markakol Reserve, yellow acacia, currant, Siberian mountain ash, forest raspberry, red elder are common; from herbaceous plants, hogweed, groundsel, ferns, geranium, sour, hedgehog, violet, woodruff and others predominate.

According to the latest data, there are more than 40 species of mammals in the reserve. Lynx, snow leopard, roe deer, squirrel, elk are well distributed. Birds are represented by the following species — common and white herons, European pelican, capercaillie, blackcock, hazel grouse, etc.

Further research of the Markakol Reserve should be aimed at developing methods for restoring the biocenosis of the taiga and studying the fish of a unique reservoir — Markakol Lake.