Cotton is a valuable fiber crop for different industries especially the textile, food and oil industries. Drought causes serious yield losses in cotton throughout the world. Association mapping reveals genomic loci controlling fiber quality and drought-related traits which will be helpful in cotton breeding because these loci can provide the genetic adaptability needed to produce good fibers and yield under water limitation. In the present study, 177 simple sequence repeat (SSR) markers were used to characterize an Upland cotton germplasm panel consisting of 99 G. hirsutum cultivars for their genetic diversity and to detect the ancestral structure of the population. Moreover, association analysis was conducted to reveal significant quantitative trait loci (QTLs) linked to a total of 22 traits for fiber quality, plant structure, yield and drought-related parameters in the panel using GLM and MLM analysis. The morphological characters were tested under both well-watered and water-limited irrigation in two locations. At both locations, GLM and MLM identified different sets of QTLs at significance level of p ≤ 0.005 and p ≤ 0.001. Of the identified QTLs, some loci were considered as stable and reliable QTLs detected in both locations. The QTLs identified herein could be useful in the development of cotton cultivars with high yield that have adaptability to drought conditions worldwide.