The current study focuses and emphasis on the potential of heat stress to negatively affect crop physiology. Here, we have screened 19 wheat (Triticum aestivum L.) genotypes for their tolerance of heat stress. Significant differences were observed among the genotypes for all the traits under consideration. Exploitable extent of genetic variability amongst the entries was present as revealed by considerably higher estimates of mean %. On the basis of Heat susceptibility Index, Halna, Mon’s Ald’s, genotypes Cuo/79/Prulla and K 307 were identified as heat-tolerant whereas SAWSN 3041, SAWSN 3101 and K 0583 were identified as heat-susceptible. The 17 wheat microsatellite markers were capable of detecting 89 alleles with an average of 4.6 alleles per locus. Polymorphism Information Content value ranged from 0.16 for the primer XGWM 516 to 0.83 for DUPW 117 with an average of 0.60. A perusal of similarity coefficients clearly reflected that a very high degree of similarity exists between wheat variety Mon’s Ald’s and SAWSN 3101 (0.70). On the other hand, the two most distantly related cultivars were found to be AKAW 4008 and PBW 343 (0.034). BARC 4, BARC 170, BARC 311, PSP 3058, WHE014.H04 and GWM 458 were strongly associated with the heat tolerance for traits TGW and BARC 311 was strongly associated with terminal heat tolerance for number of grains/plant respectively. Considering all the parameters it is adjudged that relatively stable genotypes may be evaluated at various agro climatic regions for grain yield and heat tolerance along with other contributing characters and ideal plant type.