Sustainable development of rural areas is currently receiving close attention not only in Russia, but also throughout the world. At the same time, the problem of selecting indicators and a mechanism for assessing the dynamics of sustainable development of rural areas at each level is particularly acute. No less discussion is caused by the need and possibility of polycentrical development of regions, differentiation of urban and rural areas, as well as the subjects of the Russian Federation themselves by the level of development. The purpose of this study is to develop a methodology for sustainable development of rural areas and to justify the effectiveness of its practical use in the system of implementation of regional and departmental programs and potential of local self-government. The authors propose a scenario approach as a basis for differentiation of the type of rural development: highly sustainable development, sustainable and unsustainable, which can also be applied to monitor the trajectory of long-term development, and universality of the methodology allows to apply it for all subjects of the country, regardless of their type and size. At the same time achievement of inertial scenario within the framework of unstable type of development is the basis of diagnostics of controllability and control of the subject 's strategy at the corresponding level of structural organization.