Stomatal conductance plays an important role in the heat avoidance mechanism of crop plants. Stomatal conductance in cotton is genetically determined and has been shown to be associated with heat resistance and higher yields. Experiments were carried out with six generations (parental, F1, F2 and back crosses) of three upland cotton crosses under heat-stressed and non-stressed greenhouse and field regimes, to understand the inheritance pattern of stomatal conductance as affected by contrasting temperature regimes. The results revealed significant variation for stomatal conductance due to generations and generation×temperature regime interaction in the three crosses. In general, heat stress reduced stomatal conductance and available genetic variability. Temperature regimes exerted a significant effect on the expression of the genes responsible for stomatal conductance. High temperature or heat stress favoured the expression of genes having additive effects, while absence of heat stress favoured those having dominant effects in two of the three crosses evaluated. The third cross showed the opposite reaction. The results suggest that genes controlling stomatal conductance in the parents of the first two crosses (MNH-552, HR109-RT, CIM-448, CRIS-19) were different from those controlling stomatal conductance in FH-900 and N-Karishma, the parents of the third cross. The selection efficiency of stomatal conductance in segregating populations was likely to be affected by the complexity of its inheritance, environmental dependency, and presence of substantial non-allelic and genotype×temperature regime interactions.