Chloroplast is an important organelle with autonomous genetic information in the cell.In recent years, the chloroplast genome has been used as a powerful tool for molecular markers of related species and uncovering plant evolution and phylogeny.Medicinal plants are natural resources that human beings depend on for survival and development, and the application value of chloroplast genomes in the research of medicinal plants has been widely concerned.The paper reviewed the application of the chloroplast genome in species identification and phylogenetic evolution of medicinal plants based on summarizing the research of chloroplast genome structure, providing a reference for the development and utilization of germplasm resources of medicinal plants.