﻿AbstractIn the context of the molecular phylogeny ofPolygonaceae, the phylogenetic positions of most genera and their relationships have been resolved. However, the monotypic genusHarpagocarpushas never been included in any published molecular phylogenetic studies. In the present study, we adopt a two-step approach to confirm the phylogenetic placement ofHarpagocarpususing two datasets: (1) a concatenated dataset of three chloroplast DNA (cpDNA) regions (matK,rbcLandtrnL-F) forPolygonaceaeand (2) a combinedcpDNAdataset of five sequences (accD,matK,psbA-trnH,rbcLandtrnL-F) forFagopyrum. Our analyses confirm the previous hypothesis based on morphological, anatomical and palynological investigations thatHarpagocarpusis congeneric withFagopyrumand further reveal thatH.snowdenii(≡F.snowdenii) is sister to the woody buckwheatF.tibeticum. WithinFagopyrum, three highly supported clades were discovered and the first sectional classification was proposed to accommodate them: sect.Fagopyrumcomprises the two domesticated common buckwheat (F.esculentumandF.tataricum) and their wild relatives (F.esculentumsubsp.ancestrale,F.homotropicumandF.dibotrys) which are characterised by having large corymbose inflorescences and achenes greatly exceeding the perianth; sect.Tibeticum, includingF.snowdeniiandF.tibeticum, is characterised by the achene having appurtenances along the ribs, greatly exceeding the perianth and the perianth accrescent in fruit; sect.Urophyllumcontains all other species of which the achenes were completely enclosed in the perianth. This study is very helpful to understand the phylogeny of theFagopyrumand sheds light on the future study of taxonomy, biogeography, diversification and character evolution of the genus.