The risks of uncontrolled transgenic plants penetration to southern (Mongolian) part of Altai-Sayan ecoregionare are discussed. This territory is situated along the route of massive seasonal bird migration that leads from Russia through China to countries of South Asia and back. In agriculture of China, including areas where birds stop during migration, insect resistant transgenic Bt-plants with very high contents of protein δ-endotoxins are widely used. Birds can carry seeds and uncontrolled remains of GM crops on feathers and in gastrointestinal tracts into other regions. This can lead to uncontrolled genetic contamination of the western regions of Mongolia. Thus, there is a danger of reducing species diversity of plants due to both substituting the species of local flora by GM crops and affecting the soil organisms by exposure to toxic residues of Bt-plants.