Isodon brevipedunculatus, a new species from southern China,is described and illustrated. The phylo-genetic position of the new species within the genus was analyzed based on two nuclear ribosomal DNA regions and an ingroup sampling of about 80％ of Asian species of Isodon. The results show that I. brevipedunculatus is recovered in a clade that consists of species mainly with glandular mericarps and that are distributed in the Sino-Japanese region. Combining molecular and geographical evidence, our study reveals that I. brevipedunculatus is most closely related to Isodon amethystoides and Isodon bifi-docalyx, but differs from the former in lamina shape, number of flowers per cyme, and peduncle length, and from the latter in lamina indumentum, calyx morphology, and corolla length.