Information supporting regional geoecological analysis (GEA) is one of the priority scientific fields of geography and geoecology in connection with the issues of climate change and globalization. Cartographic support of the GEA is a scientific process of translating interdisciplinary research materials into a constructive cartographic model, which requires clarifying goal-oriented theoretical issues to be studied; as well as determining the criteria for selection of empirical data and methods for their investigation; and formulating cartographic modeling methods based on the research results. The aim of the study was to develop a methodology for geographic synthesis of knowledge based on the polygeosystem concept and the idea of interpretative landscape-and-ecological mapping using GIS technologies, ranging from studying general principles and logic of research to solving specific tasks of geographic information mapping. The mapping strategy is to display the natural landscape as a complex of human living conditions in comparison with anthropogenic impact and possible consequences. The methodology for creating an outfit of landscape maps represents a combination of traditional mapping methods and geo-information ones for arranging thematic spatial data and their modification using GIS technologies. The basic principle of creating the cartographic information system (CIS) is that of complexity, it presupposes the existence of a landscape classification system, uniform for all the thematic electronic layers of the CIS, which can combine their natural and anthropogenic components. Such an approach provides a means of presenting a series of conjugated landscape-and-ecological interpretation maps of the Baikal region in the form of a holistic CIS consisting of an outfit of thematic layers, united by a common concept and created on a single landscape basis.