This article is devoted to analysis of authors' expeditionary data, as well as literature and departmental materials on the problem of monitoring and protecting biological diversity in the transboundary territories of the Russian Federation and the Republic of Kazakhstan in the south of Western Siberia. It is concluded that the state of animal populations (including rare species) is affected not only by anthropogenic, but also by natural factors, which are in particular associated with changes in the global and regional climate. Ways to increase the effectiveness of environmental measures to preserve biological diversity by creating a unified cluster network of specially protected natural areas in the border areas of Russia and Kazakhstan are proposed. We propose a unified approach to compiling registers of species that are in need of conservation, taking into account the state of their populations in the adjacent territories that are their major habitat.