A description of the bacterial communities associated with the Mediterranean pennatulids (sea pens) Pennatula phosphorea and Pteroeides spinosum from the Straits of Messina (Italy) is reported. The automated ribosomal intergenic spacer analysis showed a marked difference between coral (tissues and mucus) and non-coral (underlying sediment and surrounding water) habitats. The diversity of the coral-associated communities was more deeply analysed by sequencing the 16S rRNA genes of bacterial clones. P. phosphorea and P. spinosum harbour distinct bacterial communities, indicating the occurrence of species-specific coral-associated bacteria. In addition, only few phylotypes were shared between mucus and tissues of the same pennatulid species, suggesting that there might be a sort of microhabitat partitioning between the associated microbial communities. The predominance of Alphaproteobacteria was observed for the communities associated with both tissues and mucus of P. phosphorea (84 and 58.2 % of total sequences, respectively). Conversely, the bacterial community in the mucus layer of P. spinosum was dominated by Alphaproteobacteria (74.2 %) as opposed to the tissue library that was dominated by the Gammaproteobacteria and Mollicutes (40.6 and 35.4 %, respectively). The antibacterial activity of 78 bacterial isolates against indicator organisms was assayed. Active isolates (15.4 %), which predominantly affiliated to Vibrio spp., were mainly obtained from coral mucus. Results from the present study enlarge our knowledge on the composition and antibacterial activity of coral-associated bacterial communities.