Deep-sea research is expensive and depends heavily on technological progress much in the same way as the exploration of space. In addition, the reduced size of extreme or punctual deep-sea ecosystems make them difficult to study with conventional instrumentations deployed from surface vessels as it is done in sedimentary ecosystems.In 2004, the European Commission therefore funded a three-year project, EXOCET/D, to develop, implement and test specific instruments aimed at exploring, describing, quantifying and monitoring biodiversity in deep-sea fragmented habitats as well as at identifying links between community structure and environmental dynamics. Another objective is to develop novel data integration tools and to improve payload inter-operability. EXOCET/D involves partners from ten European research institutions and three small and medium enterprises.Here, we present the programme of the seven work packages. The working fields include: video and acoustic imagery, _in situ_ analysis of physico-chemical factors, quantitative sampling of macro- and micro-organisms, _in vivo_ experiments, integration of multidisciplinary data and implementation on European submersibles. Experimental devices onboard will complement the approach, enabling experiments on species physiology. In August 2006, the project will go into a final phase of technical and scientific field validation during the MoMARETO cruise to the Azores Triple Junction.