Owing to lack of recombination, maternal inheritance, absence of introns and higher evolutionary rates, mitochondrial DNA(mtDNA)are extensively used for population genetics, species identification and phylogenetic relationships at various taxonomic levels.In recent studies, phylogenetic analysis based on mtDNA sequence data has been proved to enhance resolution and statistical confidence of inferred phylogenetic trees when compared with traditional taxonomic methods.Taxonomy and phylogeny of Cephalopoda, which is by far one the most important economic and diversity group of mollusks, have become the most intriguing field.Herein, we provided a brief introduction to the contents and the structures of mtDNA, and subsequently reviewed the progress of mtDNA applied in cephalopod molecular systematics, especially the complete genome.Additionally, the research tendency of molecular systematics of cephalopods was discussed.