The spatial genetic structure of Polygonum thunbergii was investigated by DNA fingerprinting, using an oligonucleotide probe (GACA)₄ and restriction enzyme Dra I. The genetic similarity of DNA fingerprints among 15 plants collected over a distance of 230 m continuously decreased with increasing distance. This significant negative correlation between similarity of DNA fingerprint and distance means that there is a spatial genetic structure within the population of P. thunbergii because similarity of DNA fingerprint and genetic relatedness are strongly correlated. The genetic structure would be caused by the strictly limited seed dispersal in this species, which has cleistogamous and chasmogamous flowers with no specialized seed dispersal mechanism.