Heat stress, though primarily affects enzymes, cellular membranes and metabolic activities like respiration and photosynthesis, its damaging effect is visible through plant morphology. Plant morphology thus provides a window to invisible inside activities as well as tool to enhance resistance to heat stress. A comprehensive evaluation of over 30 cotton plant traits provided some insight on their relative importance, available genetic variability, inheritance pattern as well as comparative ability of the parental genotypes as potential donors of these traits. Heat stress favoured the expression of dominant genetic component. Cell membrane thermostability appeared to be a good screening tool rather than a breeding objective. Higher seedcotton yield, stomatal conductance and lower leaf area were observed together under heat stress, however, in its absence, higher seedcotton was more a function of higher leaf area and less of higher stomatal conductance. Seeds per boll appeared to be the most important trait, as it reflected heat tolerance at gametophytic level and showed strong link with yield.