The experience of creating a set of landscape-ecological maps for the purposes of information support of regional programs of sustainable development within the framework of electronic Environmental Atlas of the Lake Baikal watershed within two sovereign states – the Russian Federation and Mongolia is represented. Theoretical and methodological basis for the creation and structure of an integrated cartographic information system (CIS) “Landscape-ecological environment of the Lake Baikal watershed” 1 : 5 000 000 with the geosystem content are suggested. The cartographic inventory of landscape environment in the region is carried out. The results are used as an essential tool for evaluating the environmental potential of the territory. The interpreted structural, dynamic and functional characteristics of landscapes serve as limitations of nature use. They provided justification of spatial and leveled limit of anthropogenic pressures and categories of landscape protection. In general, the developed and firstly used geosystem and geoecological approach ensured the transition from the functional phase of mapping study of the natural environment of the region to the forecast of situations. The ever established mapping information system of the Lake Baikal watershed is a reflection of patterns of geographic differentiation of environmental conditions and operation of the natural environment. It can be used as a tool for information support for territory management, as well as to provide a solution of practical issues of automation of a mapping process. The CIS “Landscape-ecological environment of the Lake Baikal watershed” has the property of rapid updating of information and provides a new evaluation, forecast and recommendation maps of the environment.