The Millenium Ecosystem Assessment (2005) demonstrated that the biodiversity is the keystone for the sustainaibility of present and future ecosystems services. In spite of the highly significant effort carried out by the Census of Marine Life over the last ten years, and an increasing research effort, marine biodiversity and precise ecosystem functioning remain largely unknown and failure to reach the CBD 2010 objectives is obvious. Meanwhile, the concept of ‘ecosystem approach’ is progressing, translated into new policies such as the revised European Common Fisheries Policy (CFP). We might question if the scientific community is ready enough to built scenarios for the future and provide integrated advice to the policy makers for biodiversity conservation considering the previous uncertainties ? Key issues in term of data availability and research priorities will be discussed concomitantly to the policy agenda at the European and French levels.