AbstractAimThe Mediterranean Sea is a hotspot of endemism and it is warming at two to three times the rate of the global ocean. The continental masses that surround it constrain species range shifts. Therefore, as seawater temperature increases, distributions of marine species may contract into few small cooler refugia, with consequent risk of extinction from range contraction and fragmentation, particularly for endemics. We assess this risk for 15 molluscs of conservation concern occurring in the Mediterranean Sea. Invertebrates have been rarely assessed so far, despite their diversity and their importance for ecosystem functioning.LocationThe Mediterranean Sea and Eastern Atlantic Ocean.MethodsWe used ensemble species distribution models to project the future range of our target species and assess their IUCN Red List status.ResultsAs hypothesized, our models predicted major range shifts, contractions and fragmentation in the Mediterranean Sea for all species. Under moderate emission scenarios such as RCP4.5, up to 12 of the 15 target species will be eradicated from the eastern and southern warmer sectors. Under severe emission scenarios such as RCP8.5 and by the end of the century, we predict the global extinction of the endemic Patella ferruginea and Pinna nobilis. Non‐endemic species may buffer range loss in the Mediterranean with range gains in the Atlantic Ocean. Still, we predict that only a single species, Zonaria pyrum, will have marginal total range gains in future climate warming scenarios.Main conclusionsEight species will become threatened and the fate of Patella ferruginea and Pinna nobilis contrasts the belief that marine species are less prone to extinction than continental species under a warming climate.