The Polygonum amphibium complex (Poygonaceae) is a highly polymorphic taxon that can grow in aquatic environments as well as in moist terrestrial habitats. Aquatic and terrestrial plants of the P. amphibium complex vary significantly in morphology and exhibit very complicated patterns of morphological variation, resulting in the description of numerous infra-specific taxa. Principal components analysis of 107 individuals of the P. amphibium complex from Asia and North America using 11 morphological characters showed that the aquatic plants can be discerned from the terrestrial plants by leaf size, shape, and petiole length. In contrast, both aquatic and terrestrial plants collected from the same population or locality shared identical sequences in the matK, psbA-trnH IGS, rbcL-accD IGS and trnL-trnF regions of the chloroplast DNA (cpDNA), suggesting that aquatic and terrestrial forms of the P. amphibium complex are not genetically diverged; morphological differences between the two forms are probably due to the differences in environmental conditions of the habitats. In addition, results from the morphological analysis and the maximum parsimony analysis of the cpDNA data set revealed that the plants from Asia including Korea, Japan, China, Mongolia and Russia Far East are diverged from those in North America and Europe, suggesting that the Asian populations should be recognized as a distinct variety, P. amphibium var. amurense Korsh.