AbstractAimTo assess gaps in the representation of taxonomic, phylogenetic and functional diversity among coastal fishes inMediterranean marine‐protected areas (MPAs).LocationMediterraneanSea.MethodsWe first assessed gaps in the taxonomic representation of the 340 coastal fish species inMediterraneanMPAs, with representation targets (the species range proportion to be covered byMPAs) set to be inversely proportional to species' range sizes. We then asked whetherMPAs favoured representation of phylogenetically and functionally more distinct species or whether there was a tendency to favour less distinctive ones. We finally evaluated the overall conservation effectiveness of theMPAs using a metric that integrates species' phylogenetic and functional relationships and targets achievement. The effectiveness of theMPAsystem at protecting biodiversity was assessed by comparison of its achievements against a null model obtained by siting currentMPAs at random over the study area.ResultsAmong the coastal fish species analysed, 16 species were not covered by anyMPA. All the remaining species only partially achieved the pre‐defined representation target. The currentMPAsystem missed fewer species than expected from sitingMPAs at random. However,c. 70% of the species did not achieve better protection in the currentMPAs than expected from sitingMPAs at random. Functional and evolutionary distinctiveness were weakly correlated with target achievement. The observed coverage of taxonomic, phylogenetic and functional diversity was not different or lower than expected from sitingMPAs at random.Main conclusionsTheMediterraneanMPAsystem falls short in meeting conservation targets for coastal fish taxonomic diversity, phylogenetic diversity and functional diversity.MediterraneanMPAs do not encompass more biodiversity than expected by chance. This study reveals multiple ongoing challenges and calls for regional collaboration for the extension of theMediterranean system ofMPAs to meet international commitments and reduce the ongoing loss of marine biodiversity.