<p>The goal of the current research is to develop methodological approaches to the institutional system of regional governance targeting comprehensive social and economic development of a region. The governance system has been presented as an interconnected set of subsystems, including organizational structures (institutional system), planning and forecasting documents and a management mechanism (instruments of influence). The research makes it possible to identify the problems in integrated development which the current governance system is unable to solve or solves inefficiently. The paper features assessment of the role of the institutional governance system in implementing strategic directions of integrated regional social and economic development. It also includes an analysis of the institutional structure of spatial development management in a Russian Federation subject. The analysis involves functions, authorities, schemes and procedures used by regional governments in terms of ensuring unity and interrelation between regional and municipal levels of governance. The paper identifies the major development lines of the institutional system of regional governance ensuring integrated regional development. The research features the problems of regional integrated development and those associated with exercising authorities’ powers in regard to integrated development of territories. It has been concluded that the main problems of regional economic and social development are due to the prevalence of sectoral approach and insufficient spatial factor consideration in governance, weak spatial planning, lack of special bodies and mechanisms for managing spatial development, i.e. the lack of what should constitute the institutional system of regional governance. The authors propose recommendations to be used by the authorities on determining the powers, rights, duties and functions of institutional structures of regional governance ensuring the effectiveness of institutional governance system.</p>