The phylogenetic positions of 39 Aegilops tauschii plants with different gliadin haplotypes and collected from two habitats in Dagestan, where the species is highly variable, were defined on an intraspecies phylogenetic tree based on DNA sequences of the nuclear gene Got2. Among Ae. tauschii subsp. tauschii plants, in addition to its single major phylogenetic lineage, a plant from a rare relict lineage previously noted very far from Dagestan in Iran, Turkmenistan and Pakistan, was found. Among Ae. tauschii subsp. strangulata plant representatives, two (out of five) major lineages of this subspecies and one relict lineage were found (all these were previously found in Dagestan). Knowing that Ae. tauschii has a high migration capacity, it was very surprising not to find plants representing the other three common major lineages of subsp. strangulata, two of which are known to inhabit Azerbaijan near Dagestan. Additionally, the locations of three Ae. tauschii accessions from the Yellow River Basin (two of which are known to be native to this region) were defined on the phylogenetic tree. They were found to belong to the major lineage of Ae. tauschii subsp. tauschii. The data obtained indicate that none of the several major lineages of subsp. strangulata, which successfully coexist, have ever been able to occupy the whole subspecies distribution area throughout the species evolutionary history. In contrast, in subsp. tauschii, each (or most) of several lineages that are now relicts, occupied the whole subsp. tauschii range for some period of time in the past.