discovering the sequences of mitochondrion has made it possible to study the presence of controlling genes in this organelle. Mitochondrion is responsible for producing 90 percent of the energy that the cell needs. Some differences in the broiler chicken growing function and the resulting phenotype and food efficiency may be related to differences in mitochondrion function. The aim of this study was to clone and to analyze the ND2 gene among Khorasan’s native chickens in order to investigate possible mutations. To this end, genomic DNA was extracted from blood sample taken from this population. Then, using ND2 specific primers, PCR was conducted in order to multiply this gene. The PCR product was cloned into pTZ57R/T linear vector and sequenced. Comparison between the sequenced fragments and the registered gene revealed four mutations. A similarity of 99% was observed between them and the complete mitochondrial genome sequence of Gallus gallus with the accession numbers of X52392.1 (reference), GU261709.1, GU262712.1, AP006746.1, KF826490.1, HQ857210.1, and AY23557.1. Comparison between proteins showed that the resulting sequence was similar to protein sequences related to mitochondrial ND2 gene of the poultry in the data bank. The maximum similarity (100% similarity) was with the ND2 gene in Gallus gallus with the accession number of BAC57576.1. The minimum similarity (88% similarity) was with the ND2 gene in Chrysolophus amherstiae with the accession number of AAF65702.1 and Tetra stessewerzowi with the accession number of ABH01111.1. Also, the amino acid sequences of Khorasan’s native chicken had 99% similarity with reference sequence and other sequences with the accession numbers of YP272073.1, BAD11115.1, NP_006916.1, ADB06584.1, and ADW41566.1. After translating the obtained nucleotide sequence to the amino acid sequence, it was compared with the reference proteins sequence. The result of this comparison showed a difference in one amino acid. The amino acid Leucine 130 was changed to Methionine.