Understanding the factors relevant to endangerment and the patterns of habitat locations in relation to protected areas is critically important for the conservation of rare species. Although 64 plant species have recently been listed as endangered species in Korea, this information has, until now, not been available, making appropriate management and conservation strategies impossible to devise. Thus, we collected information on potentially threatening factors, as well as information on the locations in which these species were observed. The potentially threatening factors were classified into seven categories. National parks, provincial parks, ecosystem conservation areas, and wetland conservation areas were defined as protected conservation areas. Korean digital elevation model data, along with the maps of all protected areas were combined with the maps of endangered plant species, and analyzed via Geographic Information Systems (GIS). Excluding the category of "small population", endangered plant species in Korea were associated more frequently with extrinsic factors than intrinsic factors. Considering land surface only, all conservation areas in Korea totaled 4.9% of the land, far lower than International Union for Conservation of Nature and Natural Resources (IUCN)'s 10% coverage target. At the species level, 69% of the endangered plant species were detected in conservation areas, mostly in national parks. However, this result demonstrates that 31% of endangered species inhabit areas outside the conservation zones. Furthermore, at the habitat level, a large proportion of endangered species were found to reside in unprotected areas, revealing "gaps" in protected land. In the face of rapid environmental changes such as population increases, urbanization, and climate changes, converting these gap areas to endangered species' habitats, or at least including them in habitat networks, will help to perpetuate the existence of endangered species.