Anoectochilus malipoensis W.H. Chen & Y.M. Shui sp. nova (Orchidaceae) from Yunnan, China, is described and illustrated. It is similar to A. emeiensis but differs by having a narrow membranaceous rim in the anther cap, obovate epichile lobes with acuminate apex and crenulate margins, a narrow rim inside hypochile lobes, two 1–1.2 mm long cornua on the end of the spur, and broadly cupulate calli in the spur. These differences in flower morphology were observed in the holotype specimens. We also revise some characteristics of A. emeiensis based on examination of its holotype. The relationship between A. malipoensis and A. papillosus is discussed. Furthermore, a new identification key to the fourteen species of Anoectochilus (excluding Odontochilus) from China and Vietnam is given here.