Sheep as a domestic animal for centuries has played an important role in supplying food to people in plateau of Iran, and this geographic area is considered as the place of domestication of sheep. Study of the phylogenetic relationship of each species with other species and breeds is important in order to know more about evolution and to find solutions for the conservation of genetic reserves. Analyzing sequences of mitochondrial genome regions due to the high rate of mitochondrial genome evolution compared with the nucleus provides more reliable evidence about the genetic diversity and evolutionary origin of the species. The aim of this research was to use the sequence of mitochondrial control region to investigate the phylogenetic relationship and genetic distances between some domestic sheep breeds of Iran and some domestic sheep breeds from other Middle Eastern countries. For this purpose, blood samples were collected from Zel, Dalagh and Mehrabani sheep. After DNA extraction, polymerase chain reaction was carried out by using specific primers. Then standard sequencing was performed after purification of PCR products. Sequences obtained from this study were compared with sequences from Middle Eastern breeds registered in the NCBI. Analysis of phylogenetic tree of the main haplotypes of sheep revealed that the Zel breed with other thin-tailed breeds, such as Karayaka and Sakiz are grouped in the haplotype B. In general, most thin-tailed breeds also belong to the same haplotype. The Mehrabani breed sheep also placed in Haplotype A along with other Middle Eastern fat-tailed breeds such as Naeimi and Saidi in agreement with previous reports. This study showed that the use of the control region sequence could estimate the genetic distances in sheep breeds with high precision.

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