The article deals with problems in the application of the innovative ecosystem concept. The research is based on systems theory, innovation system theory, the theory of regional innovation systems, and the concept of open innovation. The purpose of the study is to determine the theoretical basis for applying the ecosystem concept to the development of innovation systems in regions. In the course of the study the preconditions for the formation of innovative ecosystems in the regions (acceleration of innovation; complexity of the innovation process and interdisciplinary approach to innovation; application of the concept of open innovation; acceleration of introducing the innovation to the market; possibility of functional complementarity and cooperation; possibility of joint and more efficient use of resources and infrastructure; regional differentiation; innovation risks sharing) were identified. During the work the approaches to the concept of innovation ecosystem that reflect the multidimensionality of innovation ecosystems were revealed. The article clarifies the features of the innovative ecosystems (complexity, openness, interdependence and complementarity of elements, dynamism, non-linearity) and the innovative ecosystems principles (emergence, synergy, adaptability, self-development, sustainability, self-organization, co-evolution). The study highlights the mechanisms of interactions among subjects of the innovation ecosystem (cooperation, competition, coordination, regulation, joint management) that lead to a synergetic effect for the actors of the innovation ecosystem. The obtained results systematize knowledge about innovative ecosystems and form a theoretical basis for the features of their formation and development in the regions, which can find practical application when identifying instruments of regional innovation policy.