Abstract: Expressed sequence tag derived simple sequence repeat（EST-SSR）markers for Lilium were developed and 19 polymorphic EST-SSR markers were selected to assess the phylogenetic relationships of 22 Lilium species and 74 cultivars. Phylogenetic diagram was constructed using MEGA 5.05 based on Jaccard’s genetic distance data，and principal coordinate analysis was performed to heterotic grouping of 96 accessions. The phylogenetic diagram showed that the species originated from China were first divided into two groups：GroupⅠincluded Lilium lancifolium，L. concolor，L. dauricum，L. davidii，L. leichtlinii var. maximowiczii，L. concolor var. megalanthum，L. sulphureum，L. pumilum，L. brownii var. viridulum，L. davidi var. unicdor，et al. Some of them were parents of Asiatic hybrids or Longiflorum hybrids，from which derived Asiatic hybrids，Longiflorum hybrids and LA hybrids；GroupⅡ included L. leucanthum，L. henryi，L. regale，et al. Some of them were parents of Oriental hybrids or Trumpet hybrids，from which derived Oriental hybrids，Trumpet hybrids and OT hybrids. The results mainly agreed with previous study and recorded evolutionary process of Lilium. Principal coordinate analysis was performed using NTSYS-pc2.11a. Ninety-six accessions were divided into several separate groups：Asiatic hybrids，Oriental hybrids，OT，LA and species，which in accord with known classification.

Key words: Lilium, EST-SSR, Jaccard’s genetic distance, phylogenetic tree, genetic relationship