Abstract: AIM　To analyse the genetic polymorphisms of Panax ginseng and P.quinquefolium by amplified fragment length polymorphism DNA (AFLP) molecular genetic marker technique. METHODS　Genomic DNAs extracted from dried roots of Panax ginseng and P.quinquefolium were digested by EcoRI in combination with MseI and ligated with EcoRI and MseI adapters, respectively. Meanwhile, the polymerase chain reactions were performed with E-AA and M-CAG selective primer pairs. RESULTS　The distinct, reproducible genomic DNA fingerprints were constructed using denatured polyacrylamide gel electrophoresis assay. CONCLUSION　AFLP, a powerful tool, was shown to play important roles in authentication, biological evolution, phylogenetic development of medicinal plant materials, including Panax ginseng and P.quinquefolium, and in guidance of genuine medicinal materials cultivation.