Internal transcribed spacers (ITS) of nuclear ribosomal DNA cistrons were studied in wild Lilium species native to Korea and compared with those species in the genus distributed in other countries to investigate the phylogenetic relationships among Lilium species. Sequence analysis data of Lilium plants collected from China and Japan were also included to study the inter- and intra-specific relationships in the genus. Lilium species formed a monophyletic clade and were separated in two clusters that belonged to the section Sinomartagon and Martagon. The phylogenetic relationships of Lilium species inferred from the ITS sequences using the maximum likelihood method were highly congruent with previous studies of cytogenetic evidence and classification (Comber, 1949) based on the morphological characters. The length of ITS1 and ITS2 regions in Lilium species native to Korea was uniform, however, nucleotide polymorphisms were noted. A region with a conserved sequence was observed from position 330-340 among all the species. Comparison of the sequence analysis of Lilium accessions native to different countries revealed the presence of six insertions/deletions (indels) and 121 substitutions (transitions and transversions) in both regions of ITS1 and ITS2. Indels were responsible for variation of ITS length in different accessions. The sequences of Lilium species collected from each country had less variations than those of species collected from different countries. Sequences variations in both ITS regions suggested that they could be used for assaying genetic diversity in Lilium at the inter- and intra-specific level.