Presented are the theoretical and methodological tools of creation of a data mapping system (DMS) of the natural environment for the electronic atlas of the Baikal region. The methods of GIS analysis, modification, integration and interdisciplinary integration of geographic information, as well as the structure and contents of electronic maps developed based on ideas about the ecosystems and their properties is proposed. The study was performed on the basis of literary and cartographic sources, as well as Internet resources.