This paper estimates the opportunities and willingness of regional and municipal entities on the innovation base to modify the spatial development of the Russian Federation using a systematic approach to the selection of priorities and program-project institutions of market development. The potential of the individual factors and institutions in the system of regions and territories development is reviewed; the need for program-project modernization of the federal structure of the Russian Federation is justified. Innovative direction institutions of regional development - self-development of territories, business areas, program-project planning of spatial development, etc. - are proposed.
Keywords: spatial development, institutions of program-project development management, self-development of regions and areas, strategy of program-project planning and development management