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Territory of the reserve referred to the Central Asian natural climatic range with highland Zorkul Lake of glacial origin. This lake situated on the altitude of 4100-4200 m. Within the territory of the reserve there are three more average lakes with the common name Chakankuli, which reached out along one of the gorge of Vakhan mountain ridge. Upper reaches of this ridge are referred to the territory of reserve up to the Soglasia Peak (6000 m). To the South of the lake there is the territory of Afghanistan Islamic Republic so called Afghan Badakhshan.
Climate of the reserve is high deserted, ultracontinental with extremely sharp and big daily and annual temperature fluctuation. Winter in this region is very inclement and long. Average annual temperatures is – 1,5 degrees. Absolute minimum is -47degrees. Summer is short and cool and the average temperature in July makes +13-14 degrees.
The vegetation cover of reserve is very poor. Wood vegetation is completely absent. Mountains of the reserve represented mainly by cushion-like vegetation, representing high mountain type of vegetation. Edificators of these communities related to the representatives of different life forms. Cushion-like vegetation usually represented by akantolimons and Oxytropis, which are always combined with other diverse forms of high mountain plants such as wormwood, feather grasses and others. On the humid territories cushion-like vegetation combined with cold-resistant sedges, fowl-grasses and other plants. Along streams and rivers, near to riverside of lakes and snowfields there are sedges, and cereal meadows socalled pamir sazy (waterlogged low grassed alpine meadows widespread only in the high mountain of Pamirs). Some species of sedge is habitual here (rounded, black head and others).
Zorkul Lake habited by pseudoosman and tibetian loach, and also by some species of invertebrate animals. Except the mountain Indian goose Zorkul nested by red duck, Himalayan merganser, red headed gull, Tibetan tern and other species of birds. Rodent represented by Pamir and silver field-voles, big eared pika, grey hamster, talai hare and red marmots which are very numerous here. Adjacent to Zorkul Lake mountain territory of South Amur mountain ridge inhabited by Pamir argali Marco Polo, Siberian ibexes, snow leopards, wolves and other species of fauna. Among the smaller mammals for reserve are habitual: ermine, weasel, red fox, turkestan lynx and Tian Shan brown bear. Birds of prey typical for the reserve are: bearded eagle, golden eagle and kumai.