HERMES is designed to gain new insights into the biodiversity, structure, function and dynamics of ecosystems along Europe's deep-ocean margin. It represents the first major attempt to understand European deep-water ecosystems and their environment in an integrated way by bringing together expertise in biodiversity, geology, sedimentology, physical oceanography, microbiology and biogeochemistry, so that the generic relationship between biodiversity and ecosystem functioning can be understood. Study sites will extend from the Arctic to the Black Sea and include open slopes, where landslides and deep-ocean circulation affect ecosystem development, and biodiversity hotspots, such as cold seeps, cold-water coral mounds, canyons and anoxic environments, where the geosphere and hydrosphere influence the biosphere through escape of fluids, presence of gas hydrates and deep-water currents. These important systems require urgent study because of their possible biological fragility, unique genetic resources, global relevance to carbon cycling and possible susceptibility to global change and man-made disturbances. Past changes, including catastrophic events, will be assessed using sediment archives. We will make estimates of the flow rates of methane from the geosphere and calculate how much is utilised by benthic communities, leaving the residual contribution to reach the atmosphere as a greenhouse gas. HERMES will enable forecasting of biodiversity change in relation to natural and man-made environmental changes by developing the first comprehensive pan-European margin Geographic Information System. This will provide a framework for integrating science, environmental modelling and socio-economic indicators in ecosystem management. The results will underpin the development of a comprehensive European Ocean and Seas Integrated Governance Policy enabling risk assessment, management, conservation and rehabilitation options for margin ecosystems.