In the current context of climate change, variation of sea surface temperature and salinity, sea level rise and latitudinal shifts of currents and hydrological fronts are expected to affect marine biodiversity of the sub-Antarctic Islands, particularly in coastal areas, in which many species have limited regulatory abilities. Characterizing the impact of climate change on marine communities implies that environmental data must be continuously recorded for interpreting ecological changes, predicting their potential impacts on marine life, and setting up relevant management plans. Such objectives can only be achieved by implementing a long-term and cross-disciplinary observing system. For this purpose, the IPEV program n° 1044 PROTEKER was conceived as a multidisciplinary approach including oceanographic measurements, benthic dynamics survey, as well as genetic, trophic, and eco-physiological analyses. The main objective of the program is to establish a base line for assessing the impact of climate change on coastal marine ecosystems of the Kerguelen islands by ecological and genetic monitoring at reference stations and for predicting changes in marine coastal ecosystems as a basis for vulnerability assessments and appropriate management planning. Eventually, the project aims to provide nature reserve managers and decision makers with scientific criteria for protection and conservation of KI coastal marine ecosystems. The program also aims to contribute to the international network of nearshore observing systems in the Southern Ocean (SCAR ANTOS Expert and ISSA Action Groups, IDEAL Center in Chile).