Most phenotypic traits in salmon and other commercially important marine species associated with health, growth, meat quality, and capacity for utilising new food items, have complex and partly interconnected genetic and regulatory architectures. To ensur e a continuous reduction in production costs while being able to deliver highly competitive quality products in dynamic markets requires an understanding of the underlying mechanistic basis of these traits. This initiative by the Norwegian School of Veter inary Science, University of Oslo, Norwegian Radium Hospital, Institute of Aquaculture Research and the Agricultural University of Norway aims to provide the foundation for development of the tools necessary for achieving such an understanding. We will es tablish a high-throughput SNP technology platform for disclosing genetic variation in Norwegian salmon and cattle populations. This technology platform will in addition serve a regional and partly national role concerning SNP-analyses of human, animal and plant materials, and a pilot study documenting the feasibility of the chosen technological solution will be using human material. The information generated by the SNP platform will together with other experimental data and the unique Norwegian biobank data on cattle and salmon be exploited in a sophisticated computational biology setting involving state of the art techniques for QTL localization, dynamic virtual representation of genomes, detection, description and analysis of gene re gulatory networks, and mathematical description of metabolic systems. The program builds upon and complements the current Norwegian Salmon Genome Project. It will realise several of the stated key objectives of the FUGE initiative within marine research l ike establishment of a close collaboration between industry and the research community, ensuring Norway’s leading role in the understanding and utilization of commercially interesting aspects of the salmon genome, and provide a solid national foundation for research in marine functional genomics that are strategically important to Norway.