The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen speciesLichina pygmaeaandLichina confinis, and the maritime chlorolichen speciesXanthoria aureolawhich occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. TheL. confinisandL. pygmaeacommunities were significantly different from those of the maritimeXanthoria aureolalichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notablySphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the twoLichinaspecies were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes generaRubricoccus,TunicatimonasandLewinella, suggesting an important role of these species in the marineLichinalichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.