Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, older, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown in irrigated and rainfed trials in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant differences in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in a mixed model analysis, followed by multiple regression to identify a multi-locus subset of significant markers. Multi-environment QTLs were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectively.