Abstract:The genetic diversity of 9 populations of Lilium duchartrei and 13 populations of Lilium lankongense was analyzed by inter-simple sequence repeat makers (ISSR).(1)For L.duchartrei,the percentage of polymorphic loci(PPB) at the species level,Nei’s gene diversity(H) and Shannon’s information index(Hsp) was found to be 97.26%,0.309 8 and 0.469 4,respectively,whereas for L.lankongense,the three indices were found to be 100%,0.339 0 and 0.503 0,respectively,all higher than that of L.duchartrei’s.(2)There existed little lower genetic variation at population level.The coefficient of genetic differentiation among populations(Gst) was 0.642 5 for L.duchartrei and 0.563 7 for L.lankongense,suggesting that for both species there is a high genetic differentiation among populations.(3)Both of L.duchartrei and L.lankongense,the Mantel test showed no significant correlation between genetic and geographic distances.The genetic diversities and the current genetic differentiation of L.duchartrei and L.lankongense might have resulted from combined effects,including those of life history traits and geographical isolation.(4)UPGMA analysis show significant genetic differentiation between L.duchartrei and L.lankongense at molecular level,supporting the view that they are separate species.