Salinity is one of the most serious growth limiting factor, therefore, no longer being ignored. Although, cotton is fairly salt tolerant; its sensitivity at crop stand and yield is affected. This study is planned to identify the growth, physiological and molecular parameters in local cotton varieties FDH 171 and FDH 786 under NaCl stress. There was 100% seed germination but hypocotyl length was reduced at increasing level of NaCl. Plant height, fresh and dry biomass were reduced as the plants were subjected to increased stress of NaCl. Stomatal conductance, transpiration and photosynthetic rate and ionic imbalance were found to be reduced under the gradual increase in NaCl stress and affected the plant’s overall physiological processes. PCR product of AtNHX3 has been identified in stressed and non-stressed plants. Thus, the genotypes FDH 171 & FDH 786 were found tolerant to adoption of salt stress and could be used as a source in crop improvement.