Rbcl gene of 13 Lilium species were amplified, sequenced and analyzed. By comparing the rbcL sequences with 32 other species retrieved from GenBank, the sequence divergences and the phyletic evolution were analyzed and the phylogenetic tree was constructed. All rbcL sequences across 45 species are 732 bp with an average GC content of 45.1%. Potentially parsimony informative characters (PIC) are 39. From the phylogenetic tree, it can be found that it consists of three branches which are Liliaceae Lilium (I), other Liliaceae genus (II), Trilliaceae and Palmae (III).3D model was structured by homology comparative SWISS-Model online and showed with RasTop sofeware.The evolutionary analyses from the site-specific model, the 142nd and 225th codon sites are found to be under positive selection in rbcL gene.