Process of creation and development of the special economic zones (SEZ) in regions of the Russian Federation includes a set of factors. Also other factors are distinguished from them economic, political, social, technological, legal, and geographical. In this article the geographical factor (approach) to creation and development of special economic zones in the territory of the Russian Federation is considered in more detail. In the conducted research the geographical principle of distribution of special economic zones in the territory of the Russian Federation is reasonable. On the example of South Siberia economical and geographical factors of formation of special economic zones in certain regions of the Russian Federation are defined. Work was based on the analysis of 4 special economic zones touristic – recreational type, located in the territory of Southern Siberia: “The Baikal harbor” (Republic of Buryatia), “Gate of Baikal” (Irkutsk region), “Valley of Altai” (Altai Republic), and “Turquoise Katun” (Altai Krai). By a method of strategic planning SWOT – the analysis by results of which the main problems and prospects of creation and development of special economic zones in the territory of South Siberia are defined is carried out. The received results of research can be used during further creation and development of special economic zones in the territory of this region.