Exotic Wisteria are increasingly serious invasive plants of watersheds and managed forests throughout the south-eastern United States. Naturalised individuals are frequently identified as either Wisteria floribunda or W. sinensis but may differ significantly from the original descriptions of either of those species. Here we use data from the nuclear and chloroplast genomes to determine the species classification or hybrid status of naturalised plants collected in five south-eastern states. Twenty-four of twenty-five collections (96%) were identified as hybrids between W. floribunda and W. sinensis. Haplotype analyses show that naturalised hybrid Wisteria is genetically diverse and that no relationship between haplotype and collection location exists. Morphological characters that clearly differentiate the introduced species cannot be used to reliably identify naturalised individuals. These data along with observations of the continued spread of Wisteria in the south-eastern United States suggest that hybridisation may be playing a key role in the ongoing invasion of this taxon.