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Abstract Background Accurate species delimitation is fundamental for testing evolutionary theory and provides essential implications for conservation management. The arctic-alpine genus Saxifraga L. (Saxifragaceae) is taxonomically complex and many species have not been critically assessed. The taxonomic and phylogenetic status of Saxifraga lancangensis Y.Y.Qian, considered as a synonym of Saxifraga mengtzeana Engl. & Irmsch. in previous studies, is re-evaluated in light of new evidence presented here. Results Evidence from morphological comparison and sequencing of plastid genome indicate that S. lancangensis belongs to Saxifraga sect. Irregulares Haw., and is closely related to Saxifraga geifolia Balf.f., and S. mengtzeana. However, S. lancangensis can be diagnosed by its petals with red and clawless base, leaf blade orbicular and leaf margin shallowly dentate. Conclusions The morphological and molecular evidence support the resurrection of S. lancangensis as a distinct species. An updated morphological description based on protologue and fresh material, diagnostic characters, and original photographs of the resurrected species are presented.