The Chinese endemic Polygonum schischkinii was studied from both morphological and molecular points of view. On the basis of the structure of ocreas and ocreolas, P. schischkinii appears to be a member of the genus Atraphaxis. The results of Maximum Likelihood and Bayesian analyses of combined data of the plastid [rpl32-trnL(UAG) IGS, trnL(UAA) intron, trnL-trnF IGS] and nuclear rDNA ITS1–2 regions, carried out on 61 members of tribe Polygoneae, confirmed position of P. schischkinii in the Atraphaxis clade. A new combination—Atraphaxis glareosa—based on P. glareosum, which has nomenclatural priority over P. schischkinii, is proposed. Ecological notes and a detailed distributional map of the species are also provided.