Abstract: The next-generation sequencing technology was used to obtain the whole mitochondrial genome sequences of Gadus macrocephalus. The mitochondrial gene was annotated and its structure was analyzed. The results showed that the circular genome was 16569 bp in length with typical mtDNA components. The mitochondrial genome encodes 13 proteins and 22 tRNAs, 2 rRNAs and a D-Loop region. The base composition showed a tendency of high AT and AT weak negative skewness. There were five kinds of termination codon in the protein coding gene of G. macrocephalus mitochondria, including AGG and AGA which were commonly found in mammalian mitochondria. It was shown that most of the tRNA structures share the classical clover shape, but the tRNA-Ser^(GCT) is unique because of a shortage of DHU. Two sequences with the functions of TAS and CSB, as well as 17 bp pyrimidine-rich sequences were found in D-Loop region. The non-coding region contains a conserved sequence controlling the initiation of light chain replication (O_L) and a gene spacer with 74 bp. Based on the whole mitochondrial genome sequence and the Cytb gene, the phylogenetic trees were constructed separately with several cod fish that belong to Gadiformes. The results provide an important evidence to reveal the evolutionary status of the pacific cod.