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A high level of biological diversity, including amphibians, is characteristic for Protected Areas. The group of the European green frogs has a special interest because they are characterised by unique genetic and ecological interactions in the process of hybridogenic reproduction. In 2000–2018 in the Middle Volga Region we studied green frogs in five nature reserves (Mordovia State Nature Reserve, State Nature Reserve «Prisurskiy», Volzhsko-Kamskiy State Nature Biosphere Reserve, Zhiguli State Nature Biosphere Reserve, and State Nature Reserve «Privolzhskaya lesostep'») and four national parks (National Park «Smolny», National Park «Chavash Varmane», National Park «Samarskaya Luka», and National Park «Buzulukskiy Bor»). These Protected Areas are located in a zone of overlap of ranges of Pelophylax lessonae and P. ridibundus, i.e. in area of potential spread of their meroclonal hybrid P. esculentus. Pelophylax ridibundus inhabits eight studied Protected Areas, while P. lessonae has been registered in seven and P. esculentus only in five of them. Two molecular-genetic markers were used in the study: mitochondrial COI and nuclear SAI-1. Mitotypes and alleles of two cryptic forms of P. ridibundus were revealed here, a «western» (P. ridibundus) and «eastern» (P. cf. bedriagae). In the Protected Areas we found four (of six which are possible) combinations of mitotypes of mitochondrial DNA and alleles of nuclear DNA of these two forms, and only one combination in P. esculentus. Six types of population systems of green frogs are presented in the studied Protected Areas. Single-species systems, including P. ridibundus (n = 16; 41.0%) or P. lessonae (n = 10; 25.6%), predominated. Among mixed systems a type including all three species was most common (n = 6; 15.4%). Two-species systems were the rarest: P. ridibundus and P. lessonae (n = 3; 7.7%), P. esculentus and P. lessonae (n = 3; 7.7%), P. ridibundus and P. esculentus (n = 1; 2.6%).