Achieving sustainable development of the country's energy sector, which includes many remote territories with severe natural and climatic conditions, is a complex technological and economic task, based on solving the problem of ensuring stable energy supply for all consumers. The solution of such a problem cannot be standardized for different types of territories because of their historical and evolutionary isolation. Based on the study of the reasons for the isolation, four types of isolation were identified in the research process: geopolitical, territorial, landscape and socio-economic. During the research, the world experience in the use of hybrid power supply for isolated territories of different types of isolation was studied, which was the basis for the application of the comparative approach in the development of the author's methodology for diagnosing the potential for the stability of energy systems in isolated areas. The methodology is based on author's typology of regions according to the nature of their energy systems stability, which includes seven complex indices, which make it possible to comprehensively reveal the potential for the stability of the energy systems of isolated territories. The present work presents the results of the application of the author's technique on an example of the Magadan and Sakhalin areas.