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Fallopia (Polygonaceae) as a noxious weed contains 17 species in the world out of which three species occur in Iran with invasive distribution. F. convolvulus growing in wide range of soil types causes significant problems for native ecosystems of river banks. In this study, we have examined genetic variability in F. convolvulus for the first time in Iran. Ten Inter Simple Sequence Repeats (ISSR) markers were used to study the genetic variability on 11 populations of this species. Genetic diversity parameters, genetic distance and gene flow were determined. Genetic variation at inter- and intra-population level was evaluated by different methods. AMOVA and structure analyses revealed high genetic diversity within populations. Mantel test revealed a significant correlation between genetic and geographic distances. Between populations a limited gene flow was observed. It is concluded that local adaptation, low gene exchange and genetic drift can affect genetic diversity of F. convolvulus. Despite self-compatibility of this species, it is proposed that outcrossing may occur because of higher genetic variation among populations of this taxon. [ABSTRACT FROM AUTHOR]