The distribution of legal authority to protect biodiversity in marine areas beyond national jurisdiction (ABNJ) between the Convention on Biological Diversity (CBD) and the UN Law of the Sea Convention (LOSC) has been a contentious issue. In practice, main responsibility has been allocated to LOSC, under which a new implementing agreement on conservation and sustainable use of marine biodiversity of areas beyond national jurisdiction (BBNJ) is currently being negotiated. CBD was allocated responsibility for providing scientific information and advice on marine biodiversity, which has resulted in the identification and description of 321 Ecologically or Biologically Significant Marine Areas (EBSAs) worldwide, within and beyond national jurisdiction. These could provide important scientific backing for a coming BBNJ instrument under LOSC, especially as regards the designation of marine protected areas and the conduct of environmental impact assessments in ABNJ. However, the process of modifying EBSAs and identifying new ones has recently been challenged by the CBD Conference of the Parties, harking back to previous disputes over the legal mandate and thereby threatening the entire mechanism that has been established. In the context of international environmental law and law of the sea, this article discusses the potential importance of EBSAs for the expected BBNJ instrument, using the Central Arctic Ocean EBSA as an example.