A dendrogram was constructed based on the cluster analysis of genetic similarity coefficients of genomic SSR fingerprints in all the accessions using the UPGMA method (Fig. 2). All the Aegilops tauschii and wheat accessions were clustered into three major groups. The Group I included the wheat cultivar, Chinese Spring (CS), and one Aegilops tauschii accession from Iran (SQ-222_I); Group II included nine wild Aegilops tauschii accessions from Iran; Group III encompassed other nine wild Aegilops tauschii accessions from Iran, two wild accessions from Xinjiang, and all the weedy accessions from the Yellow River region. This result in general suggested that: (1) the wheat cultivar (CS) and an Aegilops tauschii accession from Iran were closely related (with 100% of similarity coefficient), supporting the previous conclusion that Aegilops tauschii is one of the ancestral species of common wheat; (2) Aegilops tauschii accessions from different localities were considerably differentiated, and some accessions from Iran and Xinjiang shared a close genetic affinity; (3) the weedy Aegilops tauschii accessions from the Yellow River region (Shaanxi and Henan) possessed a close genetic relationship with some wild accessions from Iran, and they were closely related to each other (Fig. 2). Further analysis demonstrated significant genetic differentiation between the weedy accessions from Shaanxi and Henan within Group III, where two subgroups (Shaanxi subgroup and Henan subgroup) were clearly identified based on genetic differentiation of the accessions. The Shaanxi subgroup included all the accessions from Shaanxi, whereas the Henan subgroup included all accessions from Henan and one accession from Shaanxi. These results evidently indicated that the weedy Aegilops tauschii accessions should have been introduced directly to Chang’an (Xían) – the ancient Chinese capital that was the eastern ending point of the Silk Road, from the West (Iran) as a weed mixed with common wheat. After its introduction, the weedy Aegilops tauschii was spread out from Chang’an to other areas along the Yellow River region, together with the dispersion and cultivation of the cultivated wheat. Considerable genetic differentiations between the weedy Aegilops tauschii populations distributed in Shaanxi and Henan were developed after a long period of geographic isolation. In addition, cluster analysis indicated that genetic relationship between the weedy Aegilops tauschii accessions from Shaanxi and wild accessions from Iran was closer than that between accessions from Shaanxi and Xinjiang, of which the two wild accessions from the Yili Valley were separated in the two subgroups. The wild accession (AS-72_x) collected from Xinjiang showed the closest relationship with that from Iran, and this result was in a complete concordance with the reality that Xinjiang is the eastern boundary of the natural distribution for wild Aegilops tauschii.