The grain-ﬁlling rate plays an important role in determining grain yield. To elucidate the genetic basis of the grain-ﬁlling rate, two cultivars, Ksu106 (heat-tolerant) and Yecora Rojo (heat-sensitive) crossed and F1 and F2 populations generated. The parents, F1 and 205 F2 plants were planted on 20th January in winter season 2009 to evaluate heat tolerance during the grain-filling period. The sowing date in the present investigation represents the heat stress conditions in Saudi Arabia. The minimum number of genes or factors controlling heat tolerance was estimated (1.3) and the broad sense heritability was estimated as 30 %. The results revealed that the twelve SSR markers; Wmc24, Wmc168, Wmc326, Xgwm30, Xgwm456, Wmc25, Wmc44, Wmc94, Wmc161, Wmc273, Wmc327, and Xgwm566 were linked to grain filling rate (GFR) by quantitative trait loci (QTL) analysis of the F2 population. The results showed that regression analysis for the relationship between the twelve markers and the phenotypes of F2 individuals were highly significant. The results demonstrated that SSR markers, combined with bulked segregant analysis, could be used to identify molecular markers linked to the grain filling rate as indicator for heat tolerance in wheat.