Abstract:Despite abundant germplasm resources of wild lilies in China, the study of phylogenetic and interspecific relationship in Lilium was scarce. In this study, phylogeny of the section Leucolirion Comber which includes GenBank data and 48 specimens covering 6 closed related lilies endemic to Southwest China was explored based on ITS, cpDNA and a singlecopy nuclear gene, AKT. The results showed that: (1) in accordance with previous studies that the section Leucolirion Comber should be divided into two subsection, subsect. Leucolirion 6a and subsect. Leucolirion 6b, and L. henryi and L. rosthornii should be classified into subsect. Leucolirion 6a. We revise section Leucolirion including L. sargentiae, L. sulphureum, L. leucanthum, L. regale, L. henryi and L. rosthornii. L. bownii, which originally belonged to section Archelirion was placed into subsect. Leucolirion 6b, along with L. formosanum and L. longiflorum, we establish a new group, named section Lilium. (2)As for infrageneric relationships, section Archelirion which mainly distributes in Japan showed a sister relationship with section Leucolirion. However, section Lilium and Sinomartagon showed a close relationship. (3) The genetic distances among all taxa of chloroplast combination and AKT showed that L. henryi and L. rosthornii distinctly differ from other members of section Leucolirion. Phylogenetic tree based on chloroplast combination data, AKT fragment indicated that L. sargentiae, L. sulphureum, L. regale and L. leucanthum have a very close relationship. High genetic similarity between these species may be attributed to the particular mating system of Lilium, leading to limited genetic variation and differentiation among species.