The genetic diversity and genetic relationships of three cultivated varieties (benitade, aotade and ayutade) and a wild race of water pepper, Persicaria hydropiper, were analyzed using RAPD markers. The proportion of polymorphic bands and Shannon’s index of phenotypic diversity within accession in five benitade and two aotade accessions were distinctly lower than those in six wild water pepper accessions, suggesting the presence of a decline in genetic diversity within accession in the cultivated varieties under cultivation. A neighbor-joining (NJ) tree for nine cultivated and 38 wild accessions indicated the incidence of the independent domestication of the three cultivated varieties, benitade, aotade and ayutade, from wild water pepper. The NJ tree of the individual plants for five benitade accessions revealed the presence of close relationships among the accessions, but also showed a slight divergence in the accessions from different locations.