ABSTRACT: Epibacterial communities on thalli of the algal species Fucus serratus, Fucus vesiculosus, Laminaria saccharina, Ulva compressa, Delesseria sanguinea and Phycodrys rubens were analysed using 16S ribosomal RNA gene-based DGGE. Individuals of all species were collected in the Kiel Fjord (Baltic Sea) and in the rocky intertidal of Helgoland (North Sea). DGGE gels as well as cluster and multidimensional scaling analysis based on the DGGE band patterns of the epibacterial community showed significant differences between the epibacterial communities on the investigated algal species both in the Baltic and North Seas. Epibacterial communities differed less between regions than between host species, and were more similar on closely related host species. Results give the first evidence for lineage-specific bacterial associations to algal thalli. Furthermore, the results suggest that these algal species may control their epibiotic bacterial communities.