We acknowledge all those individuals and organisations involved in the collection of baseline samples for this project, in particular, the Central Fisheries Board of Ireland, the French National Institute for Agricultural Research (INRA), the Association of Scottish River & Fishery Management Trusts (RAFTS), the Consejeria de Medio Ambiente de Asturias (Spain) and the Environment Agency of England and Wales, who also provided the estuary-caught adult samples. This work has benefited from collaboration with a number of complementary projects being run in the UK and Ireland and we thank Arlin Rickard, Director, Association of Rivers Trusts, Dr Eric Verspoor (FRS, Pitlochry) and Dr Ken Whelan (Marine Institute, Ireland) for valuable discussions and advice throughout. We thank Ivan Gonzalez Pola and Claudia Garcia for additional help with genotyping, Anna Finnegan for constructing ArcView maps, and three anonymous referees for valuable comments on previous drafts of the manuscript. This work was funded by the European Union INTERREG IIIB programme (Atlantic Salmon Arc Project [ASAP], Project No. 040).