The objectives of the study were to develop approaches to evaluate the effectiveness of the institutional matrix of regional innovation systems from the point of view of the formation of “key” institutions for sustainable development, identification of the structural components of the “green” innovation system, their resources and functions. The methodological basis of the study was an interdisciplinary approach, including a comparative analysis of foreign and domestic scientific discourse on “green” innovation, as well as analysis of reports and studies on various aspects of the development of “green” economy and “green” innovations, case analysis, statistical data analysis, system analysis based on quantitative and qualitative approaches. The authors found that the differentiation of organizational structures of intersectoral interaction, their resource potential and functionality in the field of creation and promotion of environmental innovations determines the poly-variable nature of institutional design practices, as well as their results. The authors established possible risks of institutional development of innovation systems associated with the ongoing shift of the scientific and technological structure and social changes. Based on an empirical study of institutional practices in Russian regions, the authors identified and analyzed the main institutional mechanisms and tools that determine the success of the “scenarios” of the institutional development of eco-oriented innovation systems. It was justified the need to develop analytical tools with a set of interrelated indicators in order to adequately assess the effects of the dynamics of the regional innovation system in the context of national and global socio-economic processes. A structural model of a regional ecoinnovation system has been developed. [ABSTRACT FROM AUTHOR]