Microsatellite markers were used to analyse the biodiversity of 57 accessions of different subspecies and varieties of wild Aegilops tauschii (2n = 2x = 14; D genome) collected across the major areas where it grows in Iran. Levels of diversity were high, with numbers of alleles averaging 7.3 (ranging up to 12) and polymorphism information contents averaging 0.6591. One accession was notably more similar to two of the D genome in hexaploid wheats (Triticum aestivum) used as outgroups. Within the Ae. tauschii accessions, no markers were characteristic for taxa or geographical origin, suggesting high gene flow between the subspecies and varieties, although some groupings, which could be related to geographical origin, were evident. This survey demonstrates the high diversity present in wild goatgrass in Iran, and indicates that there is value in sampling for useful genes for wheat breeding.