Phlomoides is one of the largest genera of Lamiaceae with approximately 150–170 species distributed mainly in Eurasia. In this study, we describe and illustrate a new species, P. henryi, which was previously misidentified as P. bracteosa, from Yunnan Province, southwest China. Molecular phylogenetic analyses revealed that P. henryi is found within a clade in which most species lack basal leaves. In this clade, the new species is morphologically distinct from P. rotata in having an obvious stem and, from the rest, by having transparent to white trichomes inside the upper corolla lip. In addition, micro-features of trichomes on the calyx and leaf epidermis can differentiate the new species from other species grouped in the same clade and a key, based on trichome morphology for these species, is provided. The findings demonstrate that the use of scanning electron microscopy can reveal inconspicuous morphological affinities amongst morphologically similar species and play an important role in the taxonomic study of the genus Phlomoides.