The genetic diversity of Lilium davidii var. willmottiae selected from seven cultivated cites in Lanzhou was examined with EST-SSR markers. The results revealed a high degree of diversity at the species level, but the genetic differentiation among populations was low. Percentage of polymorphic loci was 90.91%, Nei's gene diversity was 0.3256; Shannon's information index was 0.4875;Gene flow and genetic differentiation coefficient were 1.5876 and 0.2395, respectively. The scale of genetic diversity index of the cultivated populations was as follows, Xiguoyuan > Yuzhong > Weiling > Agan > Huangyu > Jingou > Yongjing. In addition, The UPGMA cluster analysis revealed that 84.05% of materials were clustered into one group, which was consistent with the STRUCTURE results. That illustrated the narrow genetic base of L. davidii var. willmottiae. It was concluded that the genetic diversity of L. davidii var. willmottiae was mainly due to a small amount of genetic variation of germplasm. Therefore, collection and study of rare germplasm resources would provide the scientific grounds to breeding improvement and excavating elite allele gene.
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