Abstract This study compared the diversity parameters and structures of encrusting assemblages in two habitats situated at two levels of shallow rocky shore: hydrolittoral and littoral along the Baltic Sea system. We investigated the variability and level of distinctiveness of the hydrolittoral encrusting fauna based on species biodiversity and distribution, and compared these features with those of communities inhabiting the adjacent shallow littoral zone (3-m depth). Structural similarities and differences between the encrusting assemblages from adjacent hydrolittoral and littoral zones were studied within 14 locations distributed along the northern coastline of the Baltic Sea. Multivariate analysis indicates that salinity had the greatest influence on the structure of the investigated assemblages. Most of the observed hydrolittoral assemblages contained the same species as the littoral zone. This result indicated a shared common species pool with similar large-scale patterns of species distributions with some variability in the dominating species between zones. The similarity between species composition of the hydrolittoral and littoral assemblages decreased with increase of salinity. Additionally, with higher species richness and the occurrence of marine specialists adapted to hydrolittoral conditions, the role of the rock size in the frequency of species occurrence and assemblage diversity was less significant.