We present most comprehensive phylogenetic analysis of 196 accessions of Lilium representing 83 species and 14 varieties of Lilium and three outgroup genera (Cardiocrinum, Notholirion, and Fritillaria) to investigate infrageneric relationships within Lilium as well as to determine the origin and evolution of Korean species of Lilium. We used the internal transcribed spacer sequences of nuclear ribosomal DNA and phylogenetic analysis using maximum parsimony and Bayesian inference identified several major lineages within Lilium. Only one section, Martagon, turned out to be monophyletic in the study. Three sections, Archelirion, Liriotypus, and Pseudolirium, are not monophyletic because two, one, and two species in each section were placed in other lineage, respectively. Two major lineages of section Leucolirion were confirmed in this study, and as several previous studies suggested, section Sinomartagon is highly polyphyletic. The origin of Lilium hansonii, a Korean endemic to Ullung Island, is perplexing given the fact that it has ribotype of Martagon, while its cpDNA haplotype is similar to Sinomartagon. The origin of another endemic, Lilium amabile, is equally elusive and additional phylogenetic and phylogeographic studies will shed light on their evolutions in Korea. We determined that Lilium callosum var. flavum originated from L. callosum in Southern Korea.