Relationships within the Polygonaceae have been recently examined using rbcL sequences, with an emphasis on Polygonum and its segregates. Here we test these results with respect to Polygonum (sensu lato) with an expanded dataset, including additional species and gene regions. Specifically, we focus on inferring the relationships of Eupersicaria (Polygonum sect. Persicaria in many prior treatments), using the chloroplast genes rbcL, trnL–F, trnK intron–matK, and psbA–trnH IGS, and nuclear ribosomal ITS sequences. We conclude that Eupersicaria is monophyletic and most closely related to Tovara and Echinocaulon. In turn, this clade is most closely related to Cephalophilon. The sister group of this entire Persicaria clade contains Bistorta and a clade including Aconogonon and Koenigia, which supports the monophyly of the Persicarieae. Within Eupersicaria there appears to be a deep split between P. amphibia and the remaining species, and there is strong conflict regarding the placement of P. punctata. These results set the stage for a more detailed phylogenetic analysis of Eupersicaria.