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European beech-dominated natural forests are prevailing forest habitats in highland and sub mountain landscapes of the European temperate zone. Forest vegetation zone of beech forests is environmentally important for its biodiversity, which supports forest ecosystem service functioning. Conservation of natural European beech forest habitats is in the focus of conservation efforts in many European countries. This paper deals with analyses focusing on conservation efficiency of protected areas with the objective to maintain European beech-dominated natural forests. The study area covers the territory of the Czech Republic, a typical central European country. Methods of environmental assessment of conservation effectiveness of protected areas draw on the Nature Conservation Efficiency Index (NCEI) and CORINE habitats datasets analyzed by applying Geographical Information Systems (GIS). The results of analyses of the conservation efficiency of protected areas in the conservation of beech forest habitats in the Czech Republic indicate a low level of conservation efficiency. Relatively highest conservation efficiency in natural beech forests (NCEI = 0.17) is achieved only in the second zones of protected landscape areas. Although the NCEI values are still very low here, the established values have considerable potential for the future, as principles of sustainable forest management will be applied in these zones of protected landscape areas. Application of the presented method is appropriate for the environmental assessment of conservation efficiency of protected areas aimed at forest biodiversity. The results of this study also suggest that the environmental interpretation of forest land-use in GIS analyses can be used as a support tool for environmental assessment of protected areas network efficiency with the objective of maintaining European beech forest biodiversity.