Protected areas are a key component in biodiversity conservation strategies, but evaluations of how effective they are in capturing species diversity is lacking for many ecosystems. We compared different protection types (animal sanctuaries, nature reserves and unprotected areas) using data on species richness and occurrence of coastal breeding bird species in a large archipelago in the Baltic Sea. Data were from extensive inventories based on a grid with 1 × 1 km resolution covering 4646 km2 on the East coast of Sweden. We focused on specialist species breeding exclusively in coastal habitats since these species are of specific conservation concern, but considered generalists, which also breeds in inland wetlands, as well. Animal sanctuaries had significantly higher species richness of specialist species than unprotected areas and nature reserves. Nature reserves had even lower richness of specialist species than unprotected areas. Further, a rarity-weighted diversity index showed that animal sanctuaries were better in capturing hotspots of bird diversity compared to nature reserves and unprotected areas. Hotspots, both protected and unprotected, were scattered throughout the entire archipelago. The rarity-weighted richness is therefore useful to identify gaps in the protected area network. Overall, we conclude that the establishment of animal sanctuaries has been a successful conservation measure for protecting specialist species in several aspects. Ongoing human exploitation of the Baltic archipelagos prompt further consideration of protecting still unprotected but species rich shorelines for the benefit of many coastal breeding birds.