Thismia Griff. (Thismiaceae) is a holo-mycoheterotrophic genus with more than 100 species. In this study, phylogenetic analyses supported that T. malipoensis from Yunnan is a new species in T. sect. Glaziocharis. Morphologically, this new species can be distinguished from its phylogenetic sister species T. abei by having the annulus of the flower expanded and modified into a cucullate (hood-like) structure with zygomorphic symmetry with one opening on one side. Biogeographical inference showed that SW China to Indo-Burma and the Sunda Shelf region was suggested as the ancestral distribution region of Thismia s.s., then eastward to SE China and Japan, and southward to New Guinea to Australia, respectively. The Chinese species should have originated from at least two different ancestral sources, and geographical isolation caused the divergence between T. malipoensis and T. abei at 17.47 Mya.