Honey bees are important pollinators with a worldwide distribution,except in Antarctica.The mitochondrial DNA(mtDNA)of honey bee follows matrilineal inheritance,so the mtDNA characteristics of a single bee can represent the entire colony's mtDNA characteristics.Mitochondrial molecular markers have been utilized in honey bee population's genetic structure analysis to take the matrilineal genetic advantages.The advancement of restriction endonuclease and sequencing technology has led to the increased using of mitochondrial molecular marker.Here,we review the research on mtDNA genomic structure,molecular marker technology and usage in honey bees to offer insights into the evolutionary analysis of honey bees and the genetic diversity of species.