The genetic changes associated with domestication in aquaculture pose an increasing threat to the integrity of native fish gene pools. Consequently, there is a bourgeoning need for the development of molecular tools to assess and monitor the genetic impact of escaped or released farmed fish. In addition, exploration of basic links between genetic differences among farmed and wild fish and differences in important life-history traits with fitness consequences are crucial prerequisites for designing biologically informed management strategies. The project “AquaTrace” will establish an overview of current knowledge on aquaculture breeding, genomic resources and previous research projects for the marine species seabass, seabream and turbot. The project will apply cutting-edge genomic methods for the development of high-powered, cost-efficient, forensically validated and transferable DNA based tools for identifying and tracing the impact of farmed fish in the wild. Controlled experiments with wild and farmed fish and their hybrids will be conducted with salmon and brown trout as model organisms using advanced “common garden” facilities. These experiments will elucidate the fundamental consequences of introgression by pinpointing and assessing the effects on fitness of specific genomic regions. Generated insights will form the basis of a risk assessment and management recommendations including suggestions for mitigation and associated costs. This information and the developed molecular tools will be available as open-access support to project participants and external stakeholders including the aquaculture industry. The project is expected to facilitate technology transfer to the aquaculture sector by promoting better tailored breeding practices and traceability throughout production chain. Overall this initiative will support the development of sustainable European aquaculture and provide “Good Environmental Status” in line with the Marine Strategy Framework Directive.