Short Rotation Coppice (SRC) willow (genus Salix) is amongst the most advanced second generation energy crops in temperate regions due to its potential for high biomass yields in short timeframes, an ability to resprout after multiple harvests, simple and low cost propagation from cuttings and a broad genetic base. Genetic improvement programmes in Sweden and the UK have made significant progress in recent years. However, to expand production, cultivars suited to a wider range of European environments and future climates are needed. To provide markers for selection within breeding programmes, we have initiated a first association mapping project in willow, with the following key aims: 1) to establish a first willow association mapping population using European Salix viminalis germplasm; 2) to generate comparative phenotypic datasets for use in association mapping from contrasting UK and Swedish trial sites; 3) to build upon existing leads to identify candidate genes central to the achievement of high biomass yields on marginal lands and at different sites; and 4) to test variation in candidate genes for association with key yield determining traits and provide markers for use in breeding programmes. The association mapping population was established at four experimental sites in 2009 (two sites in Sweden and two in the UK) and has now been assessed for growth traits, phenology and biomass yield. Around 250 candidate genes were selected for resequencing and ~1500 SNP loci are currently being genotyped and tested for marker/trait associations.