Fish with most species of vertebrates widely distributes in various water bodies,and holds rich genetic diversity,which plays an important role in survival and evolution of fish.However,fish genetic diversity is seriously affected by various natural and artificial factors in recent years.The researches on present situation of fish genetic diversity by means of molecular markers can lay the foundation for fish genetic breeding,molecular evolution researches and protection of fish genetic resources.Nowadays,the molecular markers including mtDNA,have been applied to studying genetic structure of fish populations and the relationship between the genetic structure and related factors.In the present review,we reviewed the structure,genetic characteristics of mtDNA and its application to the molecular population genetics of fish.