Currently, agriculture is facing a great threat from the risk of climate change. The productivity of the agriculture is also being seriously affected as a significance of key changes in the pattern of temperature and rainfall. It is expected that such changes will affect water availability to plants, especially for those native to the arid and semi-arid tropics (Giorgi, 2005). The genus Gossypium L. has long focused of genetic and breeding research. Cotton was one of the first species to which the Mendelian philosophies were applied and has a long history of progress through breeding with continual long-term yield gains. For sustained cotton production under global climate change an integrated approach, involving all available resources and techniques is needed. One potential and promising part of this integrated approach is the development of crop varieties tolerant to these abiotic stresses. Molecular Association mapping techniques can be successfully used to tag the genomic regions harboring loci involved in abiotic stress tolerance in cotton to help develop cotton cultivars with promising stress tolerance. Keeping in view this objective, projects were designed to tag genomic regions involved in drought tolerance in cotton. In order to achieve such evidence in G. hirsutum, ninety genotypes of Pakistani cotton population were evaluated under well- watered and drought stress conditions for morpho-physiological, plant architecture and yield traits, under glasshouse and field on seasons 2010 and 2011 respectively. The first experiment was carried out under controlled glasshouse conditions for phenotypic variations of cotton germplasm for morpho-physiological traits. The cultivars were sown in polythene bags and arranged according to Completely Randomized Design (CRD) with four replications in each treatment. After the emergence of first true leaves, water stress was applied. Data were recorded for morpho-physiological traits. In the second experiment the genotypic responses to well irrigated (W1) and water stressed (W2) conditions were assessed under field conditions for Phenotypic variations of cotton germplasm for plant architecture and yield traits at CEMB field University of the Punjab. All ninety genotypes were evaluated in randomized complete block design (RCBD) with three replications. For molecular variations these cultivars were genotyped by using a set of ninety five SSR Maker pairs with ~3-5 marker/chromosome the study showed that microsatellite markers are efficient for measuring the genetic diversity, relatedness and identifying varieties of cotton. We performed Linkage disequilibrium (LD)-based Association mapping for morpho-physiological, plant architecture and yield cotton population using a general linear model (GLM). The genotypic data obtained from SSR screening were analyzed by software STRUCTURE2.2 for estimating subgroups in population. The phenotypic data and information about the ancestry of individuals obtained from STRUCTURE2.2 software was put in the software TASSEL 2.0.1, and then the association analysis was achieved including population structure (Q-matrix) to detect the marker genotype which associated with studied traits. In this study, from the glasshouse experiment a total of twenty three marker loci main effect were significantly associated (P < 0.05) with the morpho- physiological traits phenotyped under the drought treatment. Phenotypic variance explained (R2) value ranged from 4.7% to 19%. Highest phenotypic variance 2 explained (R ) was ascribed to NAU3011marker located in chromosome D13 associated with root length. Marker NAU3011 associated (P= 0.0012) with root length in drought treatment appeared to be a major locus as it ascribed with highest phenotypic variance explained (R2) value of 19%. Majority of the markers were found to be associated with more than one trait. NAU3414 located on chromosome A9 (Ch.9) was associated with maximum (7) number of morphological traits (shoot length, shoot fresh weight, fresh root weight, fresh plant weight, dry shoot weight, and dry plant weight). Out of total twenty three markers associated with drought treatment, nine markers were found to be common in control and drought treatment ,These markers will be helpful in future endeavors to explore the complex nature of drought tolerance in cotton and It is advised that for drought stress these markers can successfully employed for MAS in future molecular breeding programs. However From field experiments twenty marker loci were significantly associated (P < 0.05) with plant architecture and yield traits phenotyped under the drought treatment. Phenotypic variance explained (R2) value ranged from 4.26% to10.14%. Marker BNL946 (Ch.20) reported highest phenotypic variance explained (R2) value of 10.14% associated with seed cotton yield. There were twelve markers which found to be common in control and drought treatment. BNL946 D10 (Ch.20) was found to be associated with maximum number of traits (plant height, number of nodes, numbers of bolls, boll weight), this marker locus is of importance and it is recommended that this cotton genomic region is associated with plant architecture and yield traits. JESPR274 marker located in (Ch.9) is also another important locus which imparts high phenotypic variance explained (R2) value of 17.8% under control treatment. The positive results from this study encourage the further testing of these methods in different genetic systems, in the same manner as we applied to cotton. This is the first report on LD-based association mapping using G. hirsutum cultivars in Pakistan for Identification of molecular markers linked to phenotypic traits involved in drought stress tolerance. The results are helpful for application of ‘association study’ in cotton that will accelerate development of superior cotton cultivars through MAS programs.