Paraphlomis caloneura, a new species from Guangxi Zhuang Autonomous Region, China, is described and illustrated. Molecular phylogenetic analyses based on two nuclear robosomal DNA regions (ITS and ETS) and three plastid DNA markers (rpl32-trnL, rps16, and trnL-trnF) revealed that the new species is sister to P. hirsutissima. Both species are found in the limestone forests and are geographically close to each other, but P. caloneura can be easily distinguished from P. hirsutissima by its oblong or ovate-oblong and adaxially densely hispid laminas with broadly cuneate to cordate bases, densely hispid petioles, and slightly 2-lobed margins of upper corolla lips.