A number of important research projects on functional genomics in aquaculture species have been funded in the context of the Fifth and Sixth Framework Programmes. Each of these projects examined various aspects of reproduction, growth, disease resistance and other factors in different types of fish and shellfish. Rather than focus simply on the individual advances made, the EU sought to gather the entire set of research results into a single entity. This was made possible by the EU-funded 'Integrated knowledge on functional genomics in sustainable aquaculture' (Aquafunc) project. The first step was to establish a working group that consisted of representatives from all the relevant FP5 and FP6 projects. This group gathered several times for discussions on how to integrate the various findings in a coherent fashion that would be of value to the scientific community. In the end, a database was designed and populated with information from these projects. The Aquafunc database was put online, though access to the data is controlled. A pilot project was carried out for the common trout whereby extensive genomic data was uploaded and made available for analyses using a range of bioinformatic tools. A strategy for extending the pilot project results to other species was subsequently developed. A scientific publication dedicated to Aquafunc was also issued. Another valuable project outcome was the strengthening of ties among various research groups and laboratories. It is hoped that overlap can be reduced and synergies can be enhanced while delivering on the promise of a sustainable future for aquaculture in Europe.