Panax notoginseng is a cultivated ginseng species highly valued for its various pharmacological activities mostly associated with triterpenoid saponin glycosides. It would be of great interest to understand biodiversity in this ginseng species after its long history of domestication.We collected 92 random sampled 3-year-old P notoginseng plants from 4 counties of Wenshan prefecture in Yunnan province, China and documented their morphological features of plant height, stem color, number of leaves/leaflets and dry weight of tap root. Their genetic diversity was evaluated by fluorescent amplified fragment length polymorphism (fAFLP) analysis.Among the samples collected, variable morphological features were observed. For these 4 populations (Zhulijie, Shangliuhe, Bazai and Jinbuhuan) analyzed by fAFLP, percentage of polymorphic bands among the total number of 582 discrete bands were 74.05%, 45.36%, 38.83% and 51.89% respectively. Mean genetic heterozygosity were 0.166, 0.093, 0.094 and 0.125. On the other hand, Nei genetic distances among populations were all <0.03. Further analysis of molecular variance (AMOVA) attributed most (93.5%) genetic diversity to within population variation. Principal coordinates analysis (PCA) did not group any population distinctively.This domesticated ginseng species still maintains a fair level of biodiversity and this conclusion is consistent with the local practice of non-selective collection of seeds for next season planting. There was no genetic drift in populations. Biodiversity of P notoginseng can be exploited to improve this important herb through breeding. Two possible strategies include inbreeding for pure lines and hybrid breeding with genetic divergent parents for hybrid vigor.