Water availability is a primary factor limiting the distribution and abundance of plants, and provides an important opportunity to connect molecular polymorphisms to the performance and fitness of plants in their environments. We are studying molecular physiological ecology of local adaptation to drought in Boechera holboellii and in Brachypodium distachyon. We have compared water use efficiency in two B. holboellii populations from contrasting water environments, and found that genotypes from the drier site had higher water use efficiency, which was attributable to a large reduction in transpirational water loss. Expression profiling also showed significant changes in gene expression between wet and dry treatments. We are now examining a large quantitative trait locus mapping population to identify the genes which control physiological adaptation to wet and dry conditions in the field.