Along with the increased anthropogenic load on landscapes, which consists of ecological damage, the rate of destruction and extinction of biological species (and sometimes even entire ecosystems) is also growing. Therefore, the most important task of the study is to substantiate the systems of specially protected natural areas, which together must contain all the landscape diversity. It is important to realize that the system of protected areas will be effective when it is a single network integrated into the life of the local community, providing not only the exclusion of areas from economic turnover but also the organization of rational, scientifically sound economic activities to form a cultural landscape. Thus, it is necessary to investigate and generalize the mechanisms that form the landscape and ecological foundation for the organization of regional systems of protected areas for their further effective use in the organization of specially protected natural areas, which became the purpose of this study. This article provides recommendations for the organization of regional systems of specially protected natural areas and specific conditions of their landscape and ecological exploitation for the conservation of biodiversity.