In order to perform breeding programs and improve production of native chickens, preserving genetic di-versity in different areas of Iran is important due to the reduced available population. Genome sequencing is considered the most functional approach to determine the phylogeny relation between close populations. The aim of the present study was the evaluation of the phylogeny and genetic nucleotide sequences of ATP 6 and a partial region of ATP 8 fragments in mitochondrial genome of khorasanian native chickens. For this purpose, blood samples were randomly collected from6 khorasanian native chickens and after DNA extraction the ATP 6 and partial region of ATP 8 fragments with the length of 867 bp were amplified using specific primers. Sequencing was don according to Sanger method and based on automate system. The phylogeny tree and matrices of the genetic distances between khorasanian native chickens and other breeds for ATP 6 and ATP 8 of mitochondrial genome were drawn using the same sequences of mitochondrial genome in other available breeds in NCBI database. Results showed no haplotype difference between the studied samples sequences. Phylogeny test results revealed hat khorasanian native chicken were similar to native chicken in Laos, White Leghorn and White Plymouth Rock. Further more, the lowest genetic distance was observed between khorasanian native chicken with Phasianus colchicus and Tragopan caboti for the ATP 6and Columba livia and Francolinus pintadeanus for the ATP 8 genes.