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Effective protection of highly mobile and data-poor species constitutes a great challenge amid growing ocean exploitation and use. Blue whales and bowhead whales in the North-East Atlantic face several threats, such as climate change, ship strikes, pollution, and entanglement in fishing gear. Consequently, the OSPAR ("Oslo-Paris Convention for the Protection of the Marine Environment of the North-East Atlantic") Commission recognised their need for protection and included them on the OSPAR List of Threatened and/or Declining Species. Two actions to protect these endangered species that OSPAR Contracting Parties have agreed on are (i) identifying areas that play an essential role in the species' life cycle—subsequently called key habitats, and (ii) ensuring that those key habitats are covered by OSPAR marine protected areas (MPAs). In addition, OSPAR has committed to expanding its network of MPAs and other effective area-based conservation measures by 2030 to cover at least 30% of the OSPAR maritime area (termed the 30 × 30 target) from today's approx. 11%. In this paper, we present the results of modelling key habitats for the bowhead and blue whales in the North-East Atlantic, including Arctic waters. Due to the sparse data situation for these species, we apply presence-only modelling methods. As this method can, in principle, produce somewhat biased results, we recommend that systematic, regular surveys on these species in Arctic waters be significantly intensified for future analyses to overcome the data paucity and allow using presence–absence/count data modelling approaches. Key habitats of blue whales were identified between Iceland and Svalbard, extending to the Azores. For bowhead whales, key habitats were identified in the Fram Strait. However, our findings show that only 11.8% of blue whale key habitats and 4.1% of bowhead whale key habitats are currently covered by OSPAR MPAs. To protect 30% of key habitats for these species in the most efficient way, our analyses suggest that suitable areas to designate new OSPAR MPAs are located around the Azores for blue whales and in the Fram Strait for bowhead whales. With these additional MPAs, OSPAR would substantially improve the protection of the two endangered species and, at the same time, progress towards its 30 × 30 target. [ABSTRACT FROM AUTHOR]