Sixty Aegilops tauschii accessions and 60 European hexaploid wheat varieties were analyzed with 14 wheat microsatellite (WMS) primer sets to (i) study the phylogeny of Ae. tauschii, (ii) search for a specific genotype of Ae. tauschii most closely related to the D genome of hexaploid wheat, and (iii) narrow down the presumed birthplace of the latter. An average of 6.5 and 4.0 alleles per locus was detected in Ae. tauschii and in wheat, respectively. The highest genetic diversity of Ae. tauschii was found in Transcaucasia and southeast of the Caspian Sea. Distribution of the 87 alleles (without null alleles) found in Aegilops did not allow differentiation of the species into the two subspecies strangulata and tauschii. Excluding null alleles, 41 alleles occurred parallel in wheat and in Aegilops. Data obtained in this study supports the view of the D genome of hexaploid wheat being a composite of several sources but does not support subsp. strangulata as the possible major source of the D genome. The highest number of region-specific alleles (three) in Ae. tauschii occurring also in the D genome of wheat, and therefore most indicative for its evolution was found in present-day Georgia, where subsp. strangulata is not endemic.