Abstract
Lilium leichtlinii var. maximowiczii, native to Northeast Asia, shows morphological differences between Korean and Japanese varieties. This study analyzed chloroplast (cp) genomes of three diploid L. leichtlinii groups: Korean (KR), Japanese broad-leaved (JB), and Japanese narrow-leaved (JN). Genome sizes ranged from 152,053 bp to 152,588 bp with GC contents of 37.02-37.06%. All had typical quadripartite structures and contained 129 genes. Phylogenetic analysis of 48 Lilium cp genomes revealed at least three distinct L. leichtlinii varieties. Most genomic variation was found in non-coding regions, providing insights into intraspecific genomic diversity in L. leichtlinii.