Phylogenetic relationships within Polygonaceae, with an emphasis on Polygonum and segregate genera (e.g., Emex, Persicaria, Polygonella), are investigated using sequence data from the chloroplast gene rbcL. The results show the currently recognized subfamilies are likely not monophyletic. Polygonum as currently recognized is paraphyletic. Three strongly supported clades of Polygonum s.l. were found. Contained within these three clades of Polygonum s.l. are representatives of Atraphaxis, Bistorta, Koenigia and Persicaria. Other strongly supported clades found are Coccoloba, Eriogonum, Fagopyrum, Rumex and Triplaris. Patterns of character evolution were studied by mapping characters onto the phylogeny. A woody habit likely evolved multiple times within the family (in Atraphaxis, Koenigia, Muehlenbeckia, Polygonella and in the ancestor to the Eriogonum–Brunnichia clade). Quincuncial aestivation likely evolved early in the history of the family with four subsequent losses in the Rumex–Oxyria clade, Muehlenbeckia, the Eriogonum clade, and the Triplaris clade.