The availability of soil moisture is the major factor limiting wheat production. Present study was aimed to determine the physiological response of local germplasm resources of wheat exposed to different periods of water stress and rewatring at booting and grainfilling stages. The response of four wheat (Triticum aestivum L.) accessions (011251, 011417, 011320 and 011393) to water stress and exogenously applied abscisic acid (ABA) was determined in a pot study. The experiment was conducted in the wire house of Quaid-i- Azam University, Islamabad during the wheat-growing season 2005 and 2006. Pre sowing seeds treatment with ABA was made for 8 h. Water stress was imposed by withholding water supply for a period of 9 d thereafter the plants were irrigated. The first water stress treatment was started at 50% booting and the second at 50 % grainfilling. Sampling was done after 3, 6 and 9 days of induction of water stress. Recovery was studied at 48 and 72 h of re-watering. Changes in the water status of leaves along with osmoregulation, activities of antioxidant enzymes, stomatal conductance, transpiration rate, pigment, phytohormones and protein contents were measured. Yield parameters were also determined. Moreover Random Amplification of Polymorphic DNA (RAPD) analysis was done to determine the extent of genetic variability among the accessions and to evaluate the treatment induced changes in the protein profiling of grains Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) was done. Marked decreases in leaf water status, stomatal conductance, transpiration rate and contents of chlorophyll and carotenoid, Indole-3-acetic acid (IAA), Gibberellins (GA) and trans zeatin riboside (t-zr.) were associated with an increase in the accumulation of ABA (both free and bound), sugar, proline, glycine betaine and activities of antioxidant enzymes (superoxide dismutase, peroxidase and catalase) under water stress. Increase in protein content under water stress remained a dominant response except for accession 011251. The inhibitory effects of water stress were ameliorated by exogenous application of ABA and this ameliorating effect was found to be more significant at booting stage as compared to grainfilling particularly in the accession 011320. Upon rewatering the recovery from water stress was found to be greater in case of ABA treated plants. Accession 011320 was found to be the most sensitive among all xivthe accessions showing higher decrease in yield which appears to be associated with less efficient ABA metabolism as evidenced by slow accumulation of stress-induced free ABA which did not return to the pre stress level but remained significantly higher on rewatering moreover the decrease in t-zr content was also higher. Whereas, accession 011417 was found to be highly tolerant to water stress possibly by economizing water status, efficient control on the accumulation of osmolytes, stomatal conductance and activities of antioxidant enzymes concomitant with higher ABA content and lesser decrease in indole-3-acetic acid (IAA), gibberellins (GA) and trans zeatin riboside (t-zr.) contents under stress. Higher rate of recovery upon rewatering was also found in this accession. Random amplification of Polymorphic DNA (RAPD) analysis revealed a marked diversity among the four accessions and the Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) protein profiling of the grains indicated that the changes in grain protein composition are mainly controlled by genetic factors. It is inferred from the results that adverse effects of water stress in wheat become more pronounced at grain filling as compared to booting. Proline, antioxidant enzymes, ABA and t-zr content can serve as physiological markers for selecting water stress tolerant wheat genotypes. ABA seed soaking can be implicated as an effective way to alleviate the adverse effects of water stress particularly in relatively sensitive wheat genotypes.