Heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical, and molecular interventions related to these stresses for better management. The objective of this study was to study the effects of high temperature, drought and combined stresses on growth and molecular traits of Pakistani wheat genotypes. NIFA-Aman, Aas-11, TD-1 and Zamindar-04 were considered as tolerant varieties while Pirsabak-13, Kiran-95, Punjab-11 and TJ-83 were found as sensitive varieties under different stresses on the basis of agronomic traits and stress indices. Twelve selected SSR markers for heat and drought tolerance were screened in wheat genotypes. Genetic diversity and association with different agronomic traits were also determined. Marker-trait association showed that Xgwm-108 and Xgwm-617 had maximum association (five) with different traits while Xbarc-121 and Xbarc-285 showed association with a single trait. Thus, Xgwm-108 and Xgwm-617 SSR markers associated with different traits can be used for marker assisted selection in wheat breeding programme. The identified SSR markers could be valuable genomic resources for genetic/association mapping of heat and drought tolerance in wheat.