Drought is one of the major abiotic stresses affecting crop plants. Molecular genetics integrated with conventional breeding techniques has an immense potential to improve quantitative traits related to drought tolerance. Thirty-seven upland cotton (Gossypium hirsutum) genotypes/cultivars were screened for drought tolerance. Four contrasting genotypes/cultivars for drought tolerance (FH 207 and FH 910 tolerant while FH 901 and CIM 443 were susceptible) were selected. The F1, F2, BC1 and BC2 populations along with their respective parents were evaluated in the field under well watered and drought stress conditions for physiological and morphological traits. In generation means analysis, all the traits exhibited additive, dominance and interaction type of gene action. In generation variance analysis additive into environmental or additive, dominance and environmental models were fit for most of the traits except stomatal size and stomatal frequency which exhibited interaction. In correlation studies number of bolls per plant correlated positively with plant height and relative water content under well watered and drought stress conditions in both crosses. Relative water content correlated positively with cell membrane stability and correlated negatively with excised leaf water loss under drought stress. Cell membrane stability correlated negatively with excised leaf water loss under drought stress. Stomatal size correlated negatively with stomatal frequency under well watered and drought stress conditions. Fibre fineness correlated negatively with fibre length under drought stress. The F2 population of the cross FH-207 × FH-901along with the parents was also grown in pots under drought stress for QTL mapping study. The drought stress was developed by using restricted irrigation. A total of 2365 SSR primers were used to identify polymorphism between the two parents. In the primers, 100 were found polymorphic which were used to score F2 population for QTL mapping. Nine QTLs were identified on seven chromosomes. Two QTLs were identified for relative water content on chromosome A5. Two QTLs were identified on chromosome A7, one for plant height and one for excised leaf water loss. One QTL was identified for cell membrane stability on chromosome A1, one for number of bolls per plant on chromosome A10, one for boll weight on chromosome D11, one for stomatal size on chromosome A6 and one for stomatal frequency on chromosome A13. Theses QTLs may be used to breed drought tolerant cotton cultivar through marker assisted selection.