We used bulked segregant analysis (BSA) to identify microsatellite markers associated with water-stress tolerance in wheat. Two DNA pools (tolerant and sensitive) were, established from the selected F-2 individuals of crosses between water-stress-tolerant and -sensitive wheat parental genotypes on the basis of the paraquat (PQ) tolerance, leaf size, and relative water content. All three traits were previously shown to be associated with water-stress tolerance on segregating F2 progeny of the wheat crosses used in this study. Microsatellite analysis was then performed on the established DNA pools, using 35 primer pairs that included all of the chromosome group 5 (5A, 5B, 5D) markers, to detect microsatellite fragments that were present, absent, or both in the DNA pools and their parental lines. We identified one microsatellite fragment that was present in tolerant parent wheat and the tolerant bulk but absent in the sensitive parent wheat and sensitive bulk. We then followed the segregation of this marker in the tolerant F2 individuals. Use of this marker may significantly enhance the success of selection for PQ- and water-stress-tolerant genotypes in wheat breeding programs.