Isolated in the southern Indian Ocean, the Kerguelen Islands emerge from the Kerguelen-Heard Plateau on the flow of the Antarctic Circumpolar Current. They are located in a very dynamic oceanographic area positioned at the confluence between several water masses (Antarctic surface waters, Sub-Antarctic and Sub-Tropical waters) near the Antarctic convergence that tend to move southwards. Latitudinal shift of waters with other characteristics will result in environmental changes that may affect coastal biodiversity and ecosystem functioning. To be interpreted and to identify eventual trends, such changes must be recorded through the establishment of a long-term monitoring. The French Polar Institute (IPEV) PROTEKER program aims to implement such an underwater observatory that considers a multidisciplinary approach: oceanographic measurements, benthic mapping, genetic, eco-physiological, isotopic and environmental analyzes. In addition to the inventory and the monitoring of biodiversity, it also aims at providing with scientific criteria of managers in charge of protection and conservation policies (French Southern Lands National Nature Reserve). Eight sites (four in the Bay of Morbihan, two on the north coast and two on the south one) were chosen that match the following requirements: (i) representative of Sub-Antarctic habitats, (ii) accessibility compliance with the safety standards of scuba diving. Currently, temperature only is continuously measured. Results are posted on the web site www.proteker.net and updated after each campaign. The colonization dynamics are estimated from settlement clay plots revised each year (metagenomics analysis). All these results will produce models of biodiversity distribution and sensitivity to environmental changes.