Although water-limited environment is detrimental to cotton growth and productivity worldwide, development of drought tolerant cotton genotypes may improve yield in drought prone areas. The present study was aimed to examine drought tolerance of a set of Upland cotton genotypes using both empirical as well as analytical approaches, and molecular mapping of the traits conferring drought tolerance. Two field experiments and one greenhouse study were conducted in 2003 and 2004, and performance of 32 cotton genotypes for different physiological attributes conferring drought tolerance, and productivity traits were recorded under well-watered (W 1 ) and water-limited (W 2 ) regimes. Seedcotton yield (SCY) and its components were markedly affected under W 2 regime. Mean reduction in SCY due to water deficit was 20 and 43% in 2003 and 2004, respectively. Genotypes differed considerably for relative SCY losses due to water stress ranging from 20 to 74%. SCY sustainability under W 2 regime was mainly attributed to maintenance of higher boll number (BN) rather than boll weight (BW). Substantial genotypic variation for gas exchange attributes {(photosynthetic rate (P n ), stomatal conductance (g s ), and transpiration rate (E)}, osmotic adjustment (OA) cell membrane stability (CMS) existed among cotton genotypes. Water stress caused a significant reduction in gas exchange parameters in 2003 and 2004. The positive association (P<0.01) between P n and g s in both years in W 2 regime suggests a major role of stomatal effects in regulating leaf photosynthesis under water-limited conditions. P n and OA were significantly correlated with SCY (P<0.01) in W 2 regime, however, the level of associations of CMS with productivity traits was not significant. Results of green house experiment conducted to ascertain root traits in six selected genotypes demonstrated that drought tolerant genotypes possessed long tap root compared to susceptible genotypes. These findings tend to support the hypothesis that higher photosynthetic rate, maintained through OA and deep root system, leads to sustain SCY under water deficit environment. Therefore, P n and OA may be useful as selection criteria in breeding programs with the objective of improving drought tolerance and SCY under water-limited environments. For genetic analysis of drought tolerance, F 2 and F 2:3 mapping populations derived from a cross of Upland cotton genotypes RH-510 (drought tolerant) and FH-901 (drought susceptible) were evaluated for four physiological attributes, and six productivity traits, - xiv -Abstract respectively. Parent genotypes were selected on the basis of their diverse performance in screening experiments. Significant variation was found for all the traits measured except BW. Correlation analysis revealed significant association (P<0.01) of P n with g s and OA under water stress. A strong relationship (P<0.01) of SCY was found with BN in both the water regimes. Continuous variation pattern of F 2 plants and F 2:3 families for all the traits indicated that measured traits were quantitatively inherited. Transgressive segregation observed in both directions indicated that both the parents transmitted favourable alleles for each trait. Eight hundred and twenty two SSR primer pairs and 520 RAPD primers were surveyed on the genotypes which yielded 65 polymorphic loci including 33 SSRs, 30 RAPDs and two CAPSs. RAPD analysis exhibited comparatively high polymorphism (5.8%) compared to that of SSRs (4.7%). All the 65 markers were assayed on 143 F 2 plants; however, data of 51 loci were utilized for map construction due to ease in allele scoring. Linkage analysis resulted in mapping of 45 loci (24 SSRs, 20 RAPDs, one CAPS) on 10 different linkage groups. The remaining 6 markers were unlinked. Six of the linkage groups were assigned to five chromosomes of the tetraploid cotton genome. The genetic map spanned a total of 697.9 cM, covering around 15% of the total cotton genome with average inter-locus distance of 15.5 cM. QTL analysis mapped 26 QTLs impacting nine physio-economic traits. Genetic analysis of physiological traits under water-deficit stress using interval mapping (IM) and composite interval mapping (CIM) methods collectively detected nine putative QTLs, ranged from one to four for each trait. The QTL QP n 5cC located on chromosome 5 accounted for the largest phenotypic variance of 28% for P n . Interval mapping employed to determine chromosomal location of genes impacting the productivity traits yielded 12 QTLs for five traits in both water regimes. Five additional QTLs controlling these traits were identified using CIM. The information regarding QTLs discovered for the traits conferring drought tolerance, especially those explaining large amount of variation for net photosynthetic rate and osmotic adjustment, may complement breeding efforts to breed for drought tolerance in Upland cotton. Since this study constitutes first knowledge of identification of QTLs for drought tolerance in Upland cotton using F 2 and F 2:3 mapping populations, the identified QTLs need to be validated across different populations and environments before their use in marker assisted selection.