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Paraphlomis yingdeensis (Lamiaceae), a new species from the limestone area in northern Guangdong Province, China, is described and illustrated. Phylogenetic analyses, based on two nuclear DNA regions (ITS and ETS) and three plastid DNA regions (rpl32-trnL, rps16 and trnL-trnF), suggest that P. yingdeensis represents a distinct species in Paraphlomis. Morphologically, P. yingdeensis is similar to P. foliata subsp. montigena and P. nana, but can be distinguished from the former by its densely villous lamina and calyx, not decurrent base of lamina and bristle-like-acuminate apex of calyx teeth, and distinguished from the latter by its significantly taller plant (15–20 cm vs. 1–5 cm) and larger lamina (6.2–16.5 × 4–11.5 vs. 2–7 × 1.5–4 cm), densely villous stem, lamina and calyx and yellow corolla.