Wheat (Triticum aestivum L.) is one of the most vital food crops in the world. The differentiation of wheat cultivars is essential for farmers and breeders to evaluate the best quality and yield. Eight T. aestivum Asian cultivars were dealt with. The objectives of the present study are to extract data from the grain surface structures by aid of SEM and to determine genetic similarity/relatedness using Start Codon Targeted (SCoT) markers. The obtained exomorphic characters of the grains were diagnostic as they facilitated the differentiation between the studied Asian cultivars. Thirty primers were used and generated a total of 156 polymorphic loci with an average of 13 amplicons per primer. The mean of PIC and Rp have scored 0.24 and 4.6, respectively, which were at par of optimal values. Clustering and principal coordinate analyses were performed and revealed useful genetic similarities/relatedness between the studied cultivars. Trait-marker association through F-test analysis was also accomplished in this study. SEM and SCoT approaches were integral and efficient in assessing the taxonomic and genetic diversity among the cultivars under investigation. This study also investigated some Asian cultivars of the economic importance as resources for genetic improvement of T. aestivum L. in future breeding program between the developing countries.