The experiment was conducted in Department of Plant Breeding and Genetics, University of Agriculture Faisalabad to study the physio-genetic basis of drought tolerance in rice (Oryza sativa). Forty diverse rice genotypes were studied under field condition for various morphological traits in year 2008. These genotypes were evaluated for drought tolerance on the basis of physiomorphological traits and some seed traits of rice grain. From these forty genotypes twenty genotypes selected on the basis of desirable traits were grown in polythene bags to study the root shoot traits at seedling stage under normal and water stress condition for the selection of diverse parents in the year 2009. A total 28 SSR markers were also used to asses genetic diversity among the twenty genotypes of rice. More genetic diversity was observed between improved basmati rice varieties and advance breeding lines. All the 28 SSR markers showed greatest polymorphism among the rice genotypes. But some SSR markers namely RM-421, RM-254, RM-235, RM-544, RM-257, RM- 224, RM-248 and RM-590 showed highest polymorphism among the rice genotypes. Eight parents were selected on the basis of phenotypic and genotypic screening for the development of F1 hybrids by using diallel mating design to see the gene action among the parents and their F1 hybrids. All the possible combinations were made between the parents excluding reciprocals. These experiments were conducted in the green house and various morphological traits were studied under both normal and stress conditions in the year 2010. Stress was given at the reproductive stage. Data were analyzed by using Hayman graphical approach and Griffing approach to study the genetic variance and combining ability analysis among the parents and their F1 hybrids. Based on the genetic component analysis, both additive and non-additive components appeared important in the inheritance of most of the traits. Both additive and dominance type of gene action were found important in inheritance for different traits under study. Most of the traits showed constant gene action in both environments but gene action of some traits was affected by the environment. Morphological traits like Plant height, productive tillers per plant, primary branches per panicle, days to heading, days to maturity, 1000 seed weight and seed width showed over dominance type of gene action in both environments i.e. normal and drought environments. Panicle length showed over dominance only in normal irrigation conditions while seeds per panicle and seed length width ratio showed this type of gene action only in drought conditions. Some morphological traits like spikelets per spike, seed weight and seed length showed additive type of gene action in both irrigation conditions. Panicle length showed additive type of gene action in drought conditions only while seeds per panicle and length width ratio showed additive type of gene action with partial dominance only in normal irrigation conditions. From Griffing analysis genotypes CB-17, CB-32 and Basmati-198 were found good general combiners for productive tillers per plant, primary branches per panicle and yield per plant, specially under water stress condition. Maximum specific combining ability was found in Basmati- 198 × CB-17 for Productive tillers per plant, Basmati-198 × CB-42 for Primary branches per panicle and CB-32 × CB-14 for Yield per plant.