Drought stress negatively affects the cotton production all over the world. The negative impact of drought varies for different species due to some morphological and root attributes that help some species to better stand under drought. But the extent of disturbance varies for different cotton species. To find out such variation, two cotton species (Gossypium hirsutum and Gossypium arboreum) were studied under normal and drought conditions for 2 years. Two genotypes for each species were included, i.e. PC-1 and COMILLA (G. arboreum) and IUB-13 and IUB-65 (G. hirsutum). The experiment was laid out under a completely randomized design following factorial arrangement. Genotype × treatment × year interaction of cotton genotypes was studied for different root, morphological, physiological and fibre-related traits. Traits such as above ground dry biomass, above ground fresh biomass, chlorophyll contents, leaf area, seed cotton yield, sympodial branches/plant, fibre strength and ginning out-turn were higher in G. hirsutum genotypes as compared to G. arboreum genotypes. However less reduction under drought in all above mentioned traits was recorded for G. arboreum, than G. hirsutum. Furthermore, root traits; primary root length, lateral root numbers, root fresh weight and root dry weight were enriched under drought condition in G. arboreum genotypes than in G. hirsutum genotypes, which is a clear manifestation of higher drought tolerance ability in G. arboreum genotypes transferrable to G. hirsutum genotypes through interspecific crossing or other means.