Abstract:The complete mitochondrial genome sequence of the Mongolian wolf, Canis lupus chanco, was determined by the long and accurate polymerase chain reaction (L-PCR) based on the PCR fragments of primers. In order to clarify the phylogenetic position of Canis lupus chanco, we constructed the phylogenetic tree based on the concatenated 12S rRNA+16S rRNA+ 12 heavy-strand protein-coding genes of 12 Canidae animals with the genomic data obtained from GenBank. Here are the results: The entire mtDNA sequence is 16709 base pairs (bp) in length and contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one control region. A strong A-T bias was found in the nucleotide sequence of mitochondrial genome of the Mongolian wolf. All the transfer RNA genes could be folded into the typical cloverleaf-shaped structure except tRNA-Ser (AGY), which lacked the “DHU” arm. Most of the protein-coding genes have the same codon usage as other Canidae animals except COX Ⅱ gene, which terminates with the stop codon ATA. The phylogenetic analysis indicated that within the subspecies data of Canis lupus, Canis lupus laniger polarized first, then did Canis lupus arabs. Canis lupus chanco and Canis lupus lupus were sister species, which had similar phylogenetic positions.