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A new species of Gesneriaceae from Guizhou, China, Hemiboea kaiyangensis sp. nov., is described and illustrated. We investigated its phylogenetic position and relationships with 13 other species of Hemiboea C.B.Clarke, which present large morphological diversity in the genus, based on molecular analyses of the nuclear ribosomal internal transcribed spacer (ITS) and the chloroplast trnL-F intron-spacer sequences. The molecular phylogenetic analyses revealed that the new species is most closely related to H. ovalifolia. A diagnostic table and discussion of morphological characters are provided to differentiate the new species from H. longisepala, H. flaccida and H. ovalifolia.