In the article the theoretical and methodological foundations and practical results of the creation of the regional innovation system in the Arctic. The proposed methods of finding the best solutions for the management of innovation processes in territorial economic systems taking into account the heterogeneity of the external environment, which flows in the innovation process, and its inherent multidimensionality. Given a detailed analysis of the characteristics and priorities of formation and development of regional innovation systems on the example of the Yamal-Nenets Autonomous district, make recommendations for its improvement on the basis of the theoretical results. The developed methodology of system design innovation system and its infrastructural support that is tailored to the individual region and improve the pace and quality of innovation development of the region, with the elaboration of a set of standard solutions and suggestions for replication of the results in the regions of the Russian Federation.
Keywords: the Arctic zone of the Russian Federation, the innovation system and processes of the regional innovation system, control the spread of innovation, infrastructure, regulatory framework and instruments of organization of innovative activity, regional and municipal levels of innovation management, the innovation infrastructure.