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Background & Objectives: Zagros Mountains, which are between the flatlands of Mesopotamia and the Iranian plateau, surround the western border of the country. This region was the cradle of great civilizations like Mesopotamia and Elam. This study aimed to test the boundary role of the Zagros Mountains in the genetic structure of the region through evaluating the paternal lineages inheritance and patterns of genetic polymorphisms. Methods: Two hundred and ninety seven blood samples were collected from unrelated men of the different local areas of the northwest of Iran. Haplogroup frequencies were used to calculate and compare the population genetic parameters as genetic distance and genetic diversity. Results : In this research distribution time and entrance of the haplogroup G2-M406 estimated around 8800 years before present, the age of first human residential in the Zagros mountains area, Frequency of central Asian lineages in the eastern side of the mountains observed notable more than west side. While, European paternal lineages in the western side was more than eastern side of the mountains. Conclusion : This research emphasized the westward distribution and migration from Iranian plateau to the Europe through Turkey and Caucasus. This research has drown reliable phylogenetic tree of the surrounding population and showed an important geographic barrier role for these mountains to gene flow from neighboring regions and free movements of the local people. Moreover, the important role of the Zagros Mountains as a geographic barrier to gene flow from neighboring regions clearly highlighted in this research