Over the past two decades, an increasing proportion of North Atlantic salmon are dying at sea during their oceanic feeding migration. The specific reasons for the decline in this important species are as yet unknown, however, climate change is likely to be an important factor. In some rivers in the southern part of the salmons range, wild salmon now face extinction. This is in spite of unprecedented management measures to halt this decline. Arguably the greatest challenge in salmon conservation is to gain insight into the spatial and ecological use of the marine environment by different regional and river stocks, which are known to show variation in marine growth, condition, and survival. Salmon populations may migrate to different marine zones, whose environmental conditions may vary. To date it has been impossible to sample and identify the origin of sufficient numbers of wild salmon at sea to enable this vital question to be addressed. SALSEA-Merge will provide the basis for advancing our understanding of oceanic-scale, ecological and ecosystem processes. Such knowledge is fundamental to the future sustainable management of this key marine species. Through a partnership of 9 European nations the programme will deliver innovation in the areas of: genetic stock identification techniques, new genetic marker development, fine scale estimates of growth on a weekly and monthly basis, the use of novel high seas pelagic trawling technology and individual stock linked estimates of food and feeding patterns. In addition, the use of the three-dimensional Regional Ocean Modelling System, merging hydrography, oceanographic, genetic and ecological data, will deliver novel stock specific migration and distribution models. This widely supported project, provides the basis for a comprehensive investigation into the problems facing salmon at sea. It will also act as an important model for understanding the factors affecting survival of many other important marine species.