We postulates the phylogenetic relationships of section Sinomartagon using 64 Lilium taxa and two related taxa based on nucleotide sequence variations in the internal transcribed spacer regions of nuclear ribosomal DNA. Excluding the 5.8S unit, a total of 479bp were analyzed by three methods, i.e. maximum likelihood, maximum parsimony and neighbor-joining. Sinomartagon was polyphyletic and divided into five groups: (1) L. henryi, (2) L. henricii, L. macklinae, L. oxypetalum and L. nanum, (3) L. nepalense, (4) L. duchartrei, L. lankongense, L. amoenum, L. wardii and L. taliense, and (5) 10 other taxa of subsections 5a and 5b. This classification did not correspond to the subsections defined by Comber (1949), and all the groups should be recognized as distinct taxa. The second group which included mainly Nomocharis-like Lilium, should be treated as a different taxon such as section Lophophorum. Since the last group with section Dauricum and L. bulbiferum included L. davidii, the type of Sinomartagon, they could be considered to correspond to the true section Sinomartagon. The results provide a more convincing phylogenetic position for Sinomartagon.