It is now well established that climate change combined with pollution is causing profound changes in coastal marine ecosystems. These repercussions are particularly accentuated in polar environments where it has profound impact on the biodiversity, abundance and geographic distribution of populations of intertidal marine species. This is particularly true in the case of sentinel species such as the blue mussel (Mytilus spp.). Mussels are considered true “engineers” of marine ecosystem, helping to shape the biodiversity of the intertidal zones. Assessing the health status of mussels is thus of primary importance for monitoring programs. Yet, our knowledge of the impact of these environmental stresses on the biodiversity of marine coastal ecosystems remains fragmentary. In polar regions, this problem is amplified by the difficult conditions and high costs associated with sampling logistics. Building on the results of our previous campaigns at Kerguelen, we propose here to combine recent advances in the biomedical field and standard taxonomy approaches in order to establish a new sampling platform which exploits the concept of liquid biopsies collected from mussels in order to facilitate monitoring of Kerguelen’s coastal ecosystems. More specifically, we will use a new high-throughput sequencing technology for analysis of hemolymphatic circulating cell free DNA to characterize bacterial and viral microbiomes and the biodiversity of coastal marine ecosystems. A particular attention will be paid to pathogenic bacteria and viruses frequently in marine ecosystems found in densely populated. We will further carry out on-site studies to determine how physico-chemical characteristics of the ecosystems impact these microbiomes and the diversity of the ecosystem. The high-throughput sequencing approach will also allow us to confirm the presence of rare organisms and to identify new species of bacteria, viruses and marine organisms not previously identified in Kerguelen. In the long term, this project will develop new tools for monitoring the health of Kerguelen’s marine ecosystems in the face of climate change.