The genetic diversity of 10 populations of Lilium sargentiae in Yunnan Province was analyzed by phenotypic traits and inter-simple sequence repeat markers (ISSR).(1)The F values of 7 traits were from 3.26 to 19.1,which showed significant or quite significant differentiation among populations.The mean phenotypic differentiation coefficient of the 7 traits was 71.22%,and the variation among populations was higher than that within population,which indicated that the variance among populations was the main part of the phenotypic variation.(2)A total of 248 polymorphic loci were detected from 10 populations by 13 primers.The polymorphism rate was 98.80%,Nei’s gene diversity index and Shannon diversity index were 0.265 5 and 0.413 1,respectively.The gene diversity within population (H_s) was 0.175 7,and the genetic differentiation coefficient (G_st) among populations was 0.336 7.The Mantel’s test showed that there was significant correlation between genetic distance and geographical distance (r=0.804 4,P=0.009 9).The results indicated that L.sargentiae had a high level of genetic diversity at both phenotypic and molecular levels.The significant genetic differentiation existed among populations,which had obvious regional characteristics.The Ex-situ conservation was an effective method to protect L.sargentiae.