The sustainability of coral reefs bears fundamental implications to the functioning of coastal ecosystems and the biogeochemistry of our planet. The coral-associated microbiota plays a pivotal role as a fitness-enhancing factor in the survivability and persistence of the coral holobiont in marine biomes. Nevertheless, we currently lack knowledge of the taxonomy and functional traits of the highly complex microbiome that populates most coral species. Conspicuously, symbionts inhabiting octocorals which usually thrive and dominate in temperate waters have been scarcely examined. In this study, we employ a comparative metagenomics approach to uncover the distinct phylogenetic and functional features of the microbiome of temperate octocorals. To this end, high-throughput, Illumina metagenome sequencing of seawater, sediments and of the symbiotic consortium from the octocorals Eunicella verrucosa, Eunicella gazella and Leptogorgia sarmentosa was performed.