This study is to clarify influences of registrations of the world natural heritage on the system of natural resource management, in case of the mountainous region of Yakushima Island, a part of which was designated as the world natural heritage in December 1993. Some part of the mountainous region such as Johmon Cedar has been suffening from overuse since the late 1980s. After the designation, local public authorities constructed recreational facilities such as foot paths and mountain huts to prevent mountain climbers from damaging surrounding environment. Consequently, there was a rapid rise in the maintenance cost of the mountainous region from 6.09 million yen in 1992 to 64.93 million yen in 2002 (fiscal year). Several coordination institutions, furthermore, were established to enhance functional capacity of communication among the local public authorities, while these institutions made the system of natural resource management more complicated. Reports by IUCN on management of Yakushima had a huge impact on public works by the local public authorities. Concerning tourism in the protected areas, the number of visitors supported by ecotourism guides to the mountainous region has been constantly increasing. As a whole, conditions of the mountainous region have been deteriorating year by year because of overuse, despite the fact that constructions of recreational facilities as well as establishment of management system were carried out.