This paper reviews the results of several years' study by a multidisciplinary team comprising geneticists, physiologists, ecologists and statisticians of abiotic stress tolerance in barley. The strategy involves genetic fingerprinting of wild barley lines (Hordeum spontaneum C. Koch) from a range of habitats and testing these for responses to abiotic stresses under controlled conditions. Multiple regression analysis is used to identify genetic markers associated with experimentally determined stress responses. These data are related to site-of-origin ecogeographic data and used to identify areas of useful wild variation. Markers associated with traits of interest can be mapped in genetic mapping populations, revealing areas of the barley genome carrying genes controlling stress responses. This paper highlights our work on associations of amplied fragment length polymorphisms with salt tolerance and describes some initial results of the use of SSRs in studying drought tolerance in barley.