A new species of Hedyotis pubirachis is described from Guangdong province, China. It resembles H. caudatifolia in subshrub habit, lanceolate leaf blade and terminal inflorescence, but differs from the latter by its thyrsoid inflorescence with monochasial subaxes, broadly triangular calyx lobes and pubescent inflorescence rachises and capsules. Phylogenetically, Hedyotis pubirachis is close to H. effusa but they can be distinguished in the indument of the inflorescence and capsules and the length of pedicels. Pollen size dimorphism was also observed in the heterostylous flowers of the new species. The new species is provisionally assessed as Least Concern (LC), according to the IUCN Red List Categories and Criteria.