In modern geographical research, the study of transformations of geosystems occupies a special place, corresponding to the current stage of development of scientific knowledge. The study of the transformation of geosystems is based on the features of selforganization of geosystems – through the manifestation of connections and internal mechanisms, parts merge into a single space-time whole. The article presents the results of the study of the nature of self-organization of geosystems of the Southern Baikal region, which reflects the whole complex of its factors, that were formed and transformed in the process of formation of physical and geographical conditions of the territory. Their identification took into account the methodological principles of self-organization research, the features of geosystems of the region, the nature of tectonic processes, various data on climate, soils, petrological composition of rocks, permafrost, the history of the development of components of geosystems and comparison of similar landscapes. To characterize the self-organization of geosystems in the research area, the following factors were considered: inter-component relationships, interaction with the environment, and the resonance of processes. As a key area for the study, the territory of the Southern Baikal region was taken within the northern macroscline of Khamar-Daban, facing the lake Baikal, from the Khara-Murin river to the river Snow. On the basis of data synthesis, a map of the key site is compiled, which shows the nature of self-organization of geosystems, which manifests itself in three types. The first characterizes the harmonious development of the geosystem, its preservation and restoration after external influence. The second type, which is characterized by rigid relationships of components of geosystems, is associated with stagnation in the development of the geosystem, the preservation of existing relationships. The third type is determined by the destruction of inter-component and intersystem and the formation of new discrete relationships of geosystems. Within the Southern Baikal region, there is a change in the self-organization of geosystems, accompanied by the formation of rigid and discrete relationships. Anthropogenic impact reinforces the existing trends, creating conditions for rapid, often irreversible transformations of geosystems.