Abstract: Bread wheat (Triticum aestivum L.) is a major cereal crop for both human and animal food. This species is originating from the Fertile Crescent in the Middle-East. At the Neolithic period, initial germplasm was widespread by the first farmers in both Europe and East-Asia. Therefore, wheat diversity evolved under different environmental conditions and selection pressures in each continent. Today, the comparison of genetic diversity level between these two contrasted wheat germplasms may be a useful way, for both geneticists and breeders, to find new sources of variation. In this paper, 371 European and 363 Asian collections were genotyped by 38 genomic SSR and 44 EST-SSR markers. Total 865 alleles were detected, with range from 1 to 50 and a mean of 10.42. Polymorphism information content (PIC) ranged from 0 to 0.91 with an average of 0.53. Genetic diversity level in East-Asia was higher than that in Europe. European and Asian accessions were divided into two distinct sub-groups by PCO based on 83 SSR loci. The position of materials in the dendrogram was accordant with their geographical location, i.e. accessions from near geographical location were jointing into neighbours. Allele differentiation between the two continents at some loci such as Xgwm186, Xgwm257, Gpwm7433 and Gpwm7443 was very significant. This may be corresponding to the natural and breeding selection, which was supported by the marker/trait association analysis results. Chinese varieties released from 1950 to 1980 were clustered into one big group with Europeans, and far away from native landraces and varieties released before 1950. This is consistent with wheat breeding history of China. Diversity revealed by genomic SSRs was much higher than that by EST-SSRs. However, the cluster trend based on the two types of SSR was consistent. Therefore, differentiation of repetitive DNA was much rapider than functional genes in breeding selection. European germplasms can be efficiently used in Chinese wheat breeding program through backcross breeding method.