The authors analyze the challenges facing the agricultural sector of Russia, which, on the one hand, stimulate its accelerated development, including the provision of food independence of the country and, on the other hand, impose a limit on the use of the traditional ways of doing business, taking into account the contribution of the sector to global climate problems. Based on SWOT analysis there are examined the prospects of development of the model of organic agriculture. The authors identify the obstacles standing in the way of transformation of organic agriculture in the stable functioning and having significant export potential segment of the Russian economy, which is designed to ensure a balanced achievement of economic, environmental and social goals. Taking into account existing international experience, including the experience of the EU, the authors propose some additional measures of institutional support for the development of organic agriculture. The major directions of development of organic production in the various Russia's regions in view of their climatic, geographical and social characteristics are proposed.