Cephalopods are important economic marine animals not only because of high quality animal protein they supply for people, but also an vital role they play in the marine ecosystem. It is of important significance to explore their spatial distribution patterns and evolutionary history from the molecular level as cephalopods are distributed widely in three oceans and Polar seas with a great variety of species. This paper introduced the history of molecular phylogeography briefly, and illustrated its theoretical principle and practical basis. It reviewed the research progress in molecular phylogeography, and summarized population genetic structure of cephalopods and phylogeographic patterns as well as factors that influenced them. Distribution patterns of cephalopods were also disscussed from the point of view of molecular phylogeny, and the existing shortage was put forward followed by with several prospects and analysis.