This project aimed at revealing the microbial diversity associated with the rhizosphere of the seagrasses Zostera marina, Z. noltii and Cymodocea nodosa, through the sequencing of 16S rRNA amplicons using Illumina Miseq-platform. The rhizobiomes of these seagrasses were compared within one sampling site, and between two different geographical locations – Portugal and France. Besides, we evaluated differences between the rhizobiomes and their surrounding environment (i.e., bulk sediments and seawater). This study improves the understanding of microbial processes in the rhizosphere of seagrasses, highlighting the importance of bacteria involved in the sulfur cycle for the fitness of the plants.