Fishing has historically altered marine ecosystems around the Mediterranean, so that present assessments often reveal a distorted representation of past, pristine marine assemblages and food webs. Marine protected areas (MPAs), where fishing is restricted or prohibited, could provide reference information about the structure of fish assemblages under healthier (protected) conditions. Here, we collected rocky reef fish data using visual census at three MPAs in the Ligurian Sea (Bergeggi Island, Portofino, and Cinque Terre; NW Mediterranean) across a protection gradient: fully and partially protected conditions within the MPAs, and conditions open to fishing outside MPAs. Results show that: (i) fish assemblages’ structures (i.e. taxa composition and relative biomasses) change with the protection level; (ii) total fish biomass and the biomass of high-level fish predators are positively correlated with the level of protection; (iii) biomass of target species (i.e. Epinephelus marginatus, Sciaena umbra, Diplodus sargus, and D. vulgaris) are positively correlated with the protection level. In conclusion, this study shows that: (i) effective protection against fishing may allow the recovery of rocky reef fish assemblages; (ii) MPAs may enable us to better understand the structure of coastal assemblages, which are dominated in terms of biomass by high-level fish predators under healthier (protected) conditions. This study thus offers grounds for discussion of how important is the adoption of systematic ecological monitoring to assess the effectiveness of each individual MPA, but also, more importantly, to properly effectively achieve international conservation targets, such as the ‘30×30’ target, agreed by the international community.