The legal status of Biodiversity Beyond National Jurisdiction (BBNJ) has been regulated through the High Seas Treaty as a common heritage of humankind. However, there still exist problems related to overlapping areas above the Extended Continental Shelf (ECS). In such areas, a significant continental shelf would fall within national jurisdiction, whereas the water column would be under the regime of the high seas, and BBNJ would be the common heritage of humankind. We argue that, in order to address the overlapping of areas within the superjacent waters in the ECS, a given sui generis status is required, so that the coastal state has a sovereign right to conserve the BBNJ in these areas. This study concludes that the sui generis arrangement should be implemented in the context of an overlapping ECS and its water column. The efforts of the Indonesian government to extend the continental shelf beyond 200 nautical miles constitute an important step in preserving natural resources for future generations.