Polygonum sect. Tovaracomprises three morphologically very similar species; P. virginianum, P. filiforme, and P. neofiliforme. Sequences of internal transcribed spacers (ITSs) of nuclear ribosomal DNA of these were determined to examine phylogenetic relationships and the levels of differentiation among them. The size of ITS 1 was 241 bp in P. filiforme and P. neofiliforme, and 242 bp in P. virginianum. The size of ITS 2 was 243 bp in P. filiforme and P. neofiliforme, and 242 bp in P. virginianum. The size of ITS 2 was 243 bp, and that of the 5.8S ginianum from the eastern Asian species. Nucleotide divergence between them ranges from 3.3% to 3.8% for ITS 1 and from 9.3% to 10.7% for ITS 2. The molecular data also revealed that two eastern Asian species are closely related but should be treated as distinct species.