Random amplified polymorphic DNA (RAPDs) and inter-simple sequence repeats (inter-SSRs) have been used to study clonal growth and hybridization in some non-native, gynodioecious, invasive weeds from the genus Fallopia (Polygonaceae). At the study site (the River Kelvin, Glasgow, UK) a single genotype of Japanese knotweed (Fallopia japonica) was detected, consistent with all the individuals sampled being ramets of a single clone. Two genotypes of giant knotweed (F. sachalinensis) were detected, with one genotype accounting for all but one of the samples, again indicative of widespread clonal growth. Five genotypes of the hybrid between Japanese and giant knotweed (F.×bohemica) were recovered. F.×bohemica is the only male-fertile taxon present at the site and it seems probable that at least some of this genetic variation is attributable to hybrid fertility. A single plant identified using morphological methods as a backcross between F. japonica and F.×bohemica was analysed, and the molecular data were consistent with this theory. A comparison of RAPDs and inter-SSRs showed that the two techniques gave data that are broadly congruent, and both techniques showed a similar sensitivity in the number of genotypes detected.