To obtain more information on DNA fingerprintings and to confirm the genetic relationships of ten wide populations of Pinellia tornata.Collect wide-type or cultivated P. tornata from ten major production areas nation-wide as material. Twelve combinations of EcoR I and Mse I primers were used to asses divergence among ten populations. The data were analyzed using unweighted pair-group method, based on arithmetic averages (UPGMA) bootstrap analysis. Cluster analyses were performed by using NTSYSpc software version 2.1. The alkaloid was extracted from P. ternate with chlorolform and determined in UV absorption spectroscop.1,673 bands were applied with 12 combinations. These results of cluster were congruent with differences in total alkloids.The results of the study showed a potential application of AFLP fingerprinting for identification of P. ternata.