Using DNA sequencing have been used widely for analysis of phylogenetic relationships between different groups of animals. The mitochondrial DNA has evolved much faster than the nuclear DNA (nc) and therefore is more diverse compared to the nucleus DNA. Therefore, it is more efficient to identify and categorize near species. In addition, maternal inheritance of mtDNA generally results in no heterozygosity. The aim of this study was to investigate the genetic similarity between Kaboudeh, Lori-Bakhtiari and Mehrabani sheep breeds by using mitochondrial control region. it was measured by using the phylogenetic tree plot, and were examined genetic diversity among Iranian sheep and some haplotypes of foreign sheep. For this study, blood samples were collected from each breed of Iranian sheep. DNA was extracted by Guanidinium-Thiocyanate method. Primers were designed using the Primer Premier 5 software. Standard PCR was performed and PCR products were purified using ethanol precipitation and then the samples were sent for two-way sequencing. The phylogenetic tree was drawn by UMPGA method using Sequence Viewer version 7.6. Our sequences and control region sequences from other sheep breeds from different regions of the world were used. This tree showed that Kaboudeh and Mehrabani breeds were located in haplotype A and Lori-Bakhtiari breed in haplotype B.

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