Domestic animals such as sheep and goat have played a key role in food resource in Iran and These areimportant livestock species. Because they provide a good source of meat, milk, fiber and skin. Despite their importance, however, the origin and genetic study of this species remain poorly in our country. Molecular genetic data have greatly improved our ability to study the evolution of domestic mammals. Among the genetic markers mtDNA sequencing is one of the most useful and commonly employed methods for inferring phylogenetic relationships among closely related species and population. The mtDNA control region contain variable block that evolve four to five time faster than the remainder of the mtDNA molecule. In total of 43 unrelated sheep and goat blood and meat samples were collected (ovis aries [baluchi breed] N=14, ovis orientalis arkal N=8, capra hircus N=14 and capra aegagrus N=7). Nucleotide diversity and phylogenetic relationship calculated by sequencing the HVR1 segment of control region. An standard criteria for the definition of the different haplogroups was proposed based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

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