To understand the genomic characteristics among founder parents and widely grown cultivars in wheat, we screened the genomes of 4 founder parents and 4 widely grown wheat cultivars with 428 SSR markers covering the whole wheat genome. The Nei’s distances among the eight cultivars varied from 0.460 to 1.126, with an average of 0.876. The average of Nei’s distances among the founder parents was 0.955, which was higher than that among the widely grown cultivars (0.718). The alleles detected in the founder parents were over 16.4% than that presented in the widely grown cultivars. The average of alleles per SSR locus in the founder parents was 2.90, which was higher than that in the widely grown cultivars (2.43). Similarly, the means of alleles observed in the founder parents were higher than those in the widely grown cultivars on A, B and D genomes, or 19 chromosomes except of 2D and 6D. Furthermore, the founder parents had 518 specific alleles compared to widely grown cultivars, and Xwmc513 and Xbarc59 were common SSR loci. Whereas 315 specific alleles were observed in the widely grown cultivars compared to founder parents, Xpsp3029, Xwmc235, Xgwm518, Xgdm43, Xbarc146 and Xcfd80 were common SSR loci. The chromosomal regions may play an important role for the production of founder parents and widely grown wheat cultivars.