Lilium pseudonanum, a cryptic species endemic to restricted habitats within the eastern Himalayas, has been delineated from the morphologically similar Lilium nanum Klotzsch and described herein. Genetic analyses utilizing both nuclear and plastid datasets conclusively demonstrate that L. pseudonanum is an independent species that is not directly related to L. nanum, despite the two having been historically regarded as conspecific. Principal component analysis (PCA) applied to morphological data revealed no significant differences between the two species; however, it is noteworthy that L. pseudonanum exhibits larger basal leaf blades. Furthermore, the ecological niches of these two species differ significantly, with L. pseudonanum thriving in environments characterized by substantially higher summer precipitation and prolonged snow accumulation during the winter, resulting in increased moisture availability compared to the habitats of L. nanum. Utilizing environmental niche modeling (ENM), we assessed the potential range changes of L. nanum under scenarios of ongoing global warming. The projections indicate that L. nanum is likely to migrate to higher elevations, which may result in overlapping distributions with L. pseudonanum, consequently increasing the risk of habitat loss or the incorporation of L. pseudonanum into L. nanum. According to the International Union for Conservation of Nature (IUCN) Red List classification and criteria, L. pseudonanum is classified as ”Critically Endangered” (CR) due to its narrow distribution and small population size. This classification indicates that the species is at an extremely high risk of extinction and necessitates immediate and effective conservation efforts.