Abstract: Molecular anthropology is commonly defined, as the use of molecular genetics techniques in the analysis and interpretation of the patterns of genetic structure in various modern human populations; comparison of human and non-human primate genes and the retrieval of genetic information from fossil specimens to address questions that anthropologists are interested in concerning human evolution and diversity. By examining DNA sequences in different populations, molecular anthropologists can figure out how closely related those populations. Certain similarities in genetic makeup let to determine whether or not different groups of people belong to the same haplogroup and thus, if they share a common ancestor or are from the same geographical origin. This is significant because it allows anthropologists to trace back the patterns of migration and settlements which gives helpful insight, as to how contemporary populations have formed and progressed over time. Iranian and Caucasus gene pool have been at different times an important source of the Near Eastern and Eurasian Y chromosome variability, as well as a recipient of variation entered with different migratory events and the first region of the Asian continent occupied by modern humans. Consistency of genetic results with the archaeological findings or/and historical events could show a tangible and reasonable evidence to the anthropologist and may lead to the reconstruction of several stages in the history and prehistory. This essay by expression the principles of anthropology and some empirical research, examples of studding genetic structure of Iran tries to emphasize the collaboration of different fields of anthropology to detect the reasonable results and answers to questions about past and history of important regions, such as Iran.