The approaches to the creation of the Altai-Sayan ecoregion (ASER) web-atlas are presented in the article. The backgrounds promoting development of the original cartographical work, the main parts of its structure are considered. The structure of the web-atlas is based on the modularity principle. To create GIS web-atlas the following tasks were realized: development of the technology for input, store, analysis and representation of heterogeneous data; development of data structure for the web-atlas as a whole system and as the separate databases; development of geoinformation-cartographic modeling system for the evaluation and construction of map’s components; development of the technology for access to the distributed resources of the atlas using remote access technologies. ESRI software and cartographic server with open source code GeoServer have been used in this project. The cartographic data base is the background for the GIS web-atlas. In terms of content, the web-based atlas of ASER is based on the landscape approach to create environmental maps, as well as the mapping of anthropogenic factors impact, spatial mapping of socio-economic and other characteristics, environmentally protected sites and protected areas. The cartographical module of web-atlas is supplemented by science-oriented geographical descriptions, explanatory text, satellite images and photographs, diagrams and tables. Currently, a pilot version of the web-atlas for the Russian part of the ASER is under development, where the Altaisky and Katunsky reserves are taken as the model objects.