“Nanyao” is an important component of Chinese medicine resource. In recent years, provinces in the south of China have actively sought the path of the genuine regional drug industry of “Nanyao”, which has been seriously restricted by the existent problems that the species and quantity of “Nanyao” herb resources are not clear, and the germplasm resources are hard to preserve. The wild resources are severely damaged and the quality of cultivated varieties is degraded. Molecular identification technology is a new identification technique that has been widely applied in recent years, with the advantages of high accuracy and good repeatability. In this paper, the commonly used molecular identification techniques were analyzed and summarized, and the application of molecular identification techniques in “Nanyao” was analyzed from four aspects: genetic diversity analysis, genetic relationship analysis, germplasm resources evaluation, and the identification of genuine medicine, substitute, counterfeit species, multi-source one, aiming at providing the basis for the development of “Nanyao” industry.