Based on morphological and plastid data, Coptis wawushanensis (Ranunculaceae), a new species from Hongya, Sichuan, China, is described and illustrated. Phylogenetic analyses (Maximum likelihood and Bayesian inference) recover C. wawushanensis as sister to C. huanjiangensis with strong support, and place them in a well-supported clade including C. deltoidea and C. omeiensis. Morphologically, the new species most closely resembles C. omeiensis, but differs by an ovate leaf blade (vs. lanceolate to narrowly ovate), a central leaf segment 1.5–2.5× as long as the lateral segments (vs. 3–3.5×), shorter scapes (5–8 cm vs. 15–27 cm), and well-developed stolons (vs. absent). It is further distinguished from its sister species C. huanjiangensis by leaf blade shape (ovate vs. ovate-triangular), shorter scapes (5–8 cm vs. 20–32 cm), and the presence of stolons (vs. absent). An identification key to the new species and its closest relatives is provided, and its distribution and habitat are documented.