Object To research genovariations between genuine Chinese herbs and non genuine ones and to develop a valuable tool used in identification of the Chinese herb.Methods RAPD technique was applied in studies on the samples of Alisma orientalis (Sam.) Juzep. from different area in Fujian, Sichuan and Jiangxi provinces.Results The DNA fingerprints of genuine and non genuine Chinese herbs were compared and it was suggested that the herbal populations growing in different area in above three provinces had different genus characteristics.Conclusion RAPD technique is a valuable tool for identification of genuine Chinese herbs.