Consisting of approximately 30 species, the genus Paraphlomis of the mint family are mostly restricted to the subtropical area of China. In this study, Paraphlomis longicalyx, a new species from southern China, is described and illustrated. Molecular phylogenetic studies were carried out to investigate the placement of the new species within Paraphlomis based on two nuclear ribosomal DNA and four plastid DNA regions. The results show that P. longicalyx is recovered as a distinct lineage within the genus. Morphologically, the new species is similar to P. javanica and P. foliata, but can be distinguished by its densely hispidulous plants, much longer calyces, and pale-yellow corollas with reddish-purple spots on the lower lips.