Abiotic stresses is a major limiting factor in plant growth. Drought is a serious problem that affects many regions of the world, decreasing the productivity of crops worldwide. Cotton is the most valuable textile fiber crop and second oilseed crop in the world. Agriculture is the largest sector of Pakistan''s economy contributing 21% GDP. Fiber yield and lint quality is limited by drought stress after bloom. In the present work by using different molecular biological techniques six drought responsive transcripts and three full length genes have been identified from desi cotton. Their expression is also checked which showed significant over expression of these genes in drought stressed leaves as compared to control. Two genes were transformed into commercial cultivar of cotton. This work has a great impact on economy of Pakistan and will help to develop drought tolerant cotton varieties. It is need of time to develop drought tolerant crops as water shortage is becoming the major problem for the whole world.