Landscapes and ecosystems of the Earth differ not only in structural and functional features, but they response to anthropogenic impact in different ways too. Such a difference can achieve threshold values under the severe ecological conditions of the Central Asia and Southern Siberia thus defining their position in natural hierarchical natural-territorial complexes. Drastic changes in characteristics of structure and functioning lead to appearance of qualitatively new natural-anthropological systems, which are not characteristic to this geosystem zone. Anthropogenically stimulated natural processes produce ultimately mutated ecosystems. Such processes require specific attitude to ecosystems existing under severe ecological conditions at all the stages of interaction: studies, use and protection. This, in its turn demands development of ecologically sound interaction principles unified by specially designed concept of nature management and conservation of ecosystems in landscapes with severe ecological conditions.