AbstractRapid anthropogenic climate change is driving threatened biodiversity one step closer to extinction. Effects on native biodiversity are determined by an interplay between species' exposure to climate change and their specific ecological and life‐history characteristics that render them even more susceptible. Impacts on biodiversity have already been reported, however, a systematic risk evaluation of threatened marine populations is lacking. Here, we employ a trait‐based approach to assess the risk of 90 threatened marine Mediterranean species to climate change, combining species' exposure to increased sea temperature and intrinsic vulnerability. One‐quarter of the threatened marine biodiversity of the Mediterranean Sea is predicted to be under elevated levels of climate risk, with various traits identified as key vulnerability traits. High‐risk taxa including sea turtles, marine mammals, Anthozoa and Chondrichthyes are highlighted. Climate risk, vulnerability and exposure hotspots are distributed along the Western Mediterranean, Alboran, Aegean, and Adriatic Seas. At each Mediterranean marine ecoregion, 21%–31% of their threatened species have high climate risk. All Mediterranean marine protected areas host threatened species with high risk to climate change, with 90% having a minimum of 4 up to 19 species of high climate risk, making the objective of a climate‐smart conservation strategy a crucial task for immediate planning and action. Our findings aspire to offer new insights for systematic, spatially strategic planning and prioritization of vulnerable marine life in the face of accelerating climate change.