The genetic diversity of 16 Fritillaria thunbergii Miq.populations of three varieties (Xiaye,Kuanye and Duozi) distributed in Zhangshui,Yinjiang and Longguan,Yinzhou District and Ningbo of Zhejiang Province was investigated by RAPD and ISSR techniques.The results showed that:(1)The polymorphism percentages of 11 Xiaye varietes,3 Kuanye varieties and 2 Duozi varieties were 24.22%,3.81% and 0.69%,respectively.It indicated that the Xiaye variety had the highest genetic divergence and the richest genetic diversity,followed by the Kuanye variety,and the Duozi variety was the last.(2)The genetic relationship within the variety was closer than that between them.Kuanye and Duozi varieties showed a closer genetic relationship,and it was suggested that both of them may be selected from the original Xiaye variety.(3)The genetic diversity within 16 F.thunbergii Miq.populations revealed that Ht was 0.250 1±0.033 5,Hs was 0.053 2±0.009 7,G_{st was 0.787 1 and Nm was 0.135 3.The result showed that the main genetic divergence of F.thunbergii Miq.existed within the populations and the gene flow between populations was very low.}