We describe and illustrate Lilium yapingense sp. nova (Liliaceae) and show its position within the Lilium—Nomocharis complex (Liliaceae). It is similar in appearance to L. nanum but differs by (1) having no spots on the tepal bases, instead possessing symmetric stripes; (2) nectaries lacking fimbriate projections on the surfaces, but having two dark grooves; and (3) an orange-colored instead of a white bulb. Phylogenetic analyses using nuclear ITS showed that L. yapingense merits specific rank and that it is more closely related to Nomocharis than to Lilium. However, the morphological synapomorphies thought to distinguish Nomocharis from Lilium are absent from the new species. The morphology and phylogeny of L. yapingense support previous studies, which show that Nomocharis and Lilium have intergrading morphologies and that Lilium is paraphyletic with respect to Nomocharis.