The Pelagos Sanctuary is the only pelagic marine protected area in the Mediterranean Sea, instituted for the conservation of cetaceans. Considering the number and size of commercial and touristic ports located along its coasts, this protected area is highly impacted by human activities, and especially marine traffic. Fin whales and sperm whales are regularly sighted in the Pelagos Sanctuary, and ship strikes with large vessels are one of the main threats affecting these two species. Mapping hotspots of distribution along main shipping lanes could be an effective conservation tool, as they directly allow locating high risk areas. In this work, we used data collected during summer from 2009 to 2019, along main marine traffic corridors in the central region of Pelagos Sanctuary. Ship strike hotspots have been identified, considering the persistence of distribution hotspots over the 11 years period. Hotspots occurrence has then been predicted over the entire Pelagos Sanctuary area applying Generalized Additive Models, allowing for ship strike risk assessment over the marine protected area. Our results highlighted the recurrence of important areas for both species along shipping lanes characterized by high vessel traffic, identifying regions where to address conservation measures.