Submarine canyons can trap and concentrate organic falls, like terrestrial debris, including wood. Sunken wood creates a unique ecosystem in the deep sea, which base, i.e. the microbial communities directly degrading this wood, remains poorly studied. Our aim was thus to examine the wood degrading microbial community by comparing oak samples experimentally deployed in experimental mooring arrays in the Blanes Canyon (BC) and its adjacent open slope (NW Mediterranean Sea). We analyzed the microbial community by parallel tag pyrosequencing of the16S rRNA genes from wood samples recovered from different depths after 9 and 12 months of deployment. In this first study of the phylogenetic description of wood associated microbial community by high throughput molecular techniques, we found that the microbial diversity was higher in samples from BC compared to the open slope. The structure of the communities were, however, not significantly different from each other, although we observed an apparent clustering according to time of immersion. Furthermore, an in depth taxonomic analysis revealed that Alphaproteobacteria was the dominant microbial taxa, with the Roseobacter clade seeming to have a specialized role in the degradation of oak in BC and its adjacent slope.