Two new species, Hemiboea xishuiensis X.X. Bai and Hemiboea cehengensis X.X. Bai, from the karst plateau of Guizhou, China, are described here. We analyzed the molecular phylogeny of the two new species and 27 taxa within Hemiboea based on ITS and trnL-F, and the molecular phylogenetic analysis shows that the phylogenetic tree of Hemiboea forms three major clades, among these, five taxa, H. xishuiensis, H. cehengensis, H. parvibracteata W.T. Wang & Z.Yu Li, H. ovalifolia (W.T. Wang) A. Weber & Mich. Möller, and H. kaiyangensis T. Peng & S.Z.H constitute a highly supported clade (Clade II), H. fangii Chun ex Z.Yu Li occupies one clade exclusively (Clade I), and the others are clustered into the third clade (Clade III). The evolutionary analysis of morphological character in this study indicates that the involucre is not early deciduous, the calyx is 5-sect from base, the corolla is hairy outside, there are two protuberances on the inner side of abaxial surface of the corolla, and there is a ring of hairs above the base on the inner face of the corolla, the ovary is glabrous, and these characteristics may be the ancestral state of Hemiboea; H. fangii is the most primitive species of Hemiboea found to date. Meanwhile, our integrated evidence from multiple research methods shows that whether the involucre is early deciduous or not and whether there are two protuberances on the inner side of the ventral surface of the corolla may be the key characters for the classification of sections under Hemiboea, which have never been noted in the previous studies, and this finding can lay the foundation for the updated infrageneric classification of Hemiboea in the future. Furthermore, the complete plastid genomes of these two new species are reported, offering genetic resources for understanding the evolutionary history of Hemiboea.