The purpose of this study is to seek the application of IUCN categories of overlapping protected areas which is legally designated in South Korea. Different government departments in South Korea have managed and designated as protected areas. However, the protected areas due to different management agencies can be confused with restricting behaviors and supporting residents. The IUCN presents the reasonal standardization classifying the protected areas which could be applied all over the world. Six categories issued by the IUCN could be applied to deal with the problems of the overlapping protected areas. We suggested the application of the IUCN categories compared with legal frame in South Korea. Most areas are overlapped in designation, but the areas are important for ecology and landscape. Moreover, each protected areas in South Korea have zone districts. Comprehensively considered all these things, we made rationale matrix correlated with the IUCN categories and the zone districts of the protected areas in South Korea. For the result of this study, this matrix could be helped to the application of the IUCN categories in domestic protected areas. Although the protected areas has been recognized as regulatory regions, it is expected to expand and sustain the areas based on the matrix.