Aegilops tauschii Coss. is the D-genome donor to bread wheat (Triticum aestivum) and is the most promising wild species as a genetic resource for wheat breeding, when used for creating synthetic hexaploid wheat (SW). To study the population structure and diversity of 81 Ae. tauschii accessions collected from various regions of its geographical distribution, these lines were used to develop a diversity array technology (DArT) marker array. This Ae. tauschii array and a previously developed DArT wheat array were used to scan the genomes of the 81 accessions. Out of the 7500 markers 4449 were polymorphic. Phylogenetic studies revealed that the accessions could be divided into two major groups (Central Asian and Iranian), whereas population structure studies divided the accessions into two major groups and one minor group. In parallel study we compared the expression of traits at different ploidy levels and evaluated the applicability of Ae. tauschii drought-related traits using 33 Ae. tauschii accessions along with their corresponding SW lines under well-watered and drought conditions. We found wide variation in Ae. tauschii and even wide variation the SW lines. Ae. tauschii from some regions gave better performing SW lines. The traits of Ae. tauschii were not significantly correlated with their corresponding SW lines, indicating that the traits expressed in the diploid level may not predict the traits will be expressed in the SW lines. The information obtained about Ae. tauschii in the current study is useful for wheat breeding and the new DArT array from this Ae. tauschii population is expected to be an effective tool for wheat studies. We are planning to construct association maps of these lines to extract more useful information for wheat improvement.