Abstract: The phylogeny of Polygonum sect. Cephalophilon was analyzed using the chloroplast genes trnL-F, rbcL and nuclear ribosomal ITS sequences. Individual and combined analyses of three datasets were performed with maximum parsimony method and the gene trees were constructed with Rheum officinale as outgroup. The results show that Polygonum sect. Cephalophilon is a more natural group which is the most closely related to Polygonum sect. Persicaria, sect. Echinocaulon and the genus Antenoron. The results support to put Polygonum sect. Cephalophilon into the genus Persicaria as a section and transfer P.filicaule and P.cyanandrum from Polygonum sect. Cephalophilon to the genus Koenigia, do not support to attribute Polygonum sect. Echinocaulon to Polygonum sect. Cephalophilon. There is strong conflict regarding the systematic position of Polygonum delicatulum, which needs further studies.

Key words: Phylogeny, trnL-F, rbc-L, ITS, Polygonum sect. Cephalophilon, Polygonaceae