Mining and conservation are two contradict interests related to the natural resources management. This situation happens to the karst area in Gunungkidul, Yogyakarta. The landforms of Gunungkidul are mostly comprised of karst of Gunungsewu which has been acknowledged by UNESCO in September 2015 as part Global Geoparks Network that must be conserved. However, as basic material needed in some industries, karst becomes income generator for many people through rampant mining activities. This legal research will analyze the conformity of the regulations and their application on karst protection in Gunungkidul, Yogyakarta. The primary legal data are collected through observation and interview, while the secondary data are taken from the literatures in the form of primary legal material, secondary legal material and tertiary legal material. By means of qualitative descriptive analyses and comparative approach on existing regulations, this research comes to the conclusion that the issuance of The Governor of the Special Region Yogyakarta Regulation Number 31 of 2015 on The Procedures for Giving Regional Mining Permit on Mineral, Metal, Non-Metal and Rock has potentially opened mining activities within conservation areas, even though those areas have been conserved by other legislations such as The Regulation of The Minister of Energy and Mineral Resources of The Republic of Indonesia Number 17 of 2012 concerning The Karst as The Geological Conservation Area. In order to provide guidance for the provincial government in executing its authority to issue a mining permit in Gunungkidul, the clearer map excluded from conserved areas that allowed for existing and coming mining activities is suggested to be rigidly determined and legalized by the authorities with consideration of sustainable use principle.