A new species, Lilium evansii (Liliaceae family), was recently discovered in Yunnan Province, China. Although its range is nearest that of L. henrici, it exhibits the greatest morphological similarity to L. mackliniae, native to the isolated region of Manipur, India, from which it is separated by the vast Kachin Plains. By integration of morphological features and molecular phylogenetic analyses, we clarify the taxonomic placement of L. evansii. The observed discordance between nuclear ribosomal ITS and plastid analyses in resolving the phylogenetic position of this species coupled with its distribution in the Hengduan Mountains points to incomplete lineage sorting or ancient hybridization events and subsequent geographic isolation as key factors in the emergence of this species. Comparative studies using molecular phylogenetics underscore the importance of this discovery for enhancing our understanding of evolutionary processes in the Lilium-Nomocharis complex, a group that thrives in the biodiversity hotspot spanning the Hengduan Mountains and adjacent Himalayan regions.