The present study aimed to investigate salt stress response of diploid cotton (Gossypium arboreum L.) cultivars commonly cultivated in the region. The developmental, biochemical and physiological responses of desi cotton varieties FDH 171 and FDH 786 under NaCl stress (100, 150 and 200 mM) was evaluated. Root and shoot length and seedling vigor were reduced but root: shoot was gradually increased as the plants were subjected to increased stress of NaCl. Leaf relative water content and turgor potential were found to be reduced under the gradual increase in NaCl stress. Decrease in osmotic and water potential affected the plant’s overall physiological mechanism. Biochemical processes including chlorophyll content, proline and soluble sugars under salt stress justify the reduction of cellular osmotic potential. Consequently, the genotypes FDH 171 & FDH 786 were found tolerant to the adoption of salt stress. These genotypes can be an excellent source of cotton improvement programme for salinity tolerance.