Lilium shenxianjuense, a new species of Liliaceae from Zhejiang, China, is described with illustrations. Phylogenetic analysis based on complete plastomes places the new species as sister to a clade that comprises species of L. sect. Sinomartagon. Morphologically, L. shenxianjuense is like L. concolor and L. lancifolium, but differs in habitat preferences and morphology. The plastome is like those of other species of Lilium in gene content and structure. The new species is critically endangered and in need of urgent protection.