Iran, as a part of Fertile Crescent, is within the center of diversity and origin of the Triticum L. from Poaceae Barnhart (Gramineae A. L. de Jussieu) family. This study concerns the genetic diversity and inter-relationships analyses of 89 accessions of diploid Triticum (2n = 2x = 14) species including T. monococcum, T. boeoticum subsp. boeoticum, T. boeoticum subsp. thaoudar and T. urartu belong to the einkorn wheat group collected all around Iran using 8 primer pairs of IRAP (Inter-Retrotransposon Amplified Polymorphism). Of 220 DNA fragments analysed from all of accessions, 217 (98.6%) were polymorphic. The genetic distances among taxa and accessions were estimated and dendrograms showing relationship among accessions were generated. The results of this study showed that four taxa of diploid wheat are very similar to each other genetically and there is a high affinity, gene flow and genetic relationships between diploid Triticum accessions, although T. monococcum can be distinct loosely from the two other species including T. boeoticum and T. urartu. The highest average Nei genetic distances were found between T. monococcum and T. urartu (0.14) and the lowest between T. boeoticum subsp. boeoticum and T. boeoticum subsp. thaoudar (0.03). Analyssi of molecular variance (AMOVA) was revealed that 84% of total variation attributed to within population’s variability and the remaining 16% variation was ascribed to the differences among species; also it demonstrated a geographical distinction among Triticum accessions. These data proved a center of high diversity in the West and the Northwest of Iran and clearly exposed patterns of two distinct geographic regions.