Attempts to develope designation criteria for ecological protected areas were made forrational and scientific designation and management of ‘ecosystem and landscape conservationareas’, ‘wetland protection areas’, ‘special islands protection areas’, and ‘wildlife protectedareas’ which have been designated and managed by the Ministry of Environment. Throughanalysis of the requisites and criteria of IUCN, UNESCO, Natura 2000, the Ramsar convention,the United States, the United Kingdom, Japan, and Germany as well as various academicresearches, evaluation items of the protected areas were classified into naturalness, biodiversity,ecosystem, and scientific values. These classification titles are reflection of Korean lawsconcerning the 4 protected areas described above. Of these items ‘naturalness’ is composed of 3factors of wilderness, geomorphology and landscape, and vegetation. ‘Biodiversity’ iscomposed of the 5 factors of species diversity, endangered species, rare species, indigenousbiological resources, and habitat of wetland wild animals. ‘Ecosystem’ is composed of 5 factorsof typicalness, diversity, rarity, restoration ability, and degree of interference. All factors arescored using a 3 point scale of high, middle, or low and are then transformed into the numericalindex for designating and zoning purposes. Conclusively, it is expected that the developed methodology will be highly applicable with field verifications.