Accurate identification of weedy species is critical to the success of biological control programs seeking host-specific control agents. Phylogenetic relationships based on internal transcribed spacer region (ITS1, ITS2) DNA sequence data were used to elucidate the most likely origin and taxonomic placement of Senecio madagascariensis Poir. (fireweed; Asteraceae) in the Hawaiian archipelago. Putative S. madagascariensis populations from Madagascar, South Africa, Swaziland, and Hawaii were included in the analysis. Different phylogenetic models (maximum parsimony and maximum likelihood) were congruent in suggesting that Hawaiian fireweed is most closely related to populations from the KwaZulu-Natal region in South Africa. Phylogenetic divergence and morphological data (achene characteristics) suggest that the S. madagascariensis complex is in need of revised alpha-level taxonomy. Taxonomic identity of invasive fireweed in Hawaii is important for finding effective biological control agents as native range populations constitute different biotypic variants across a wide geographical area. Based on our phylogenetic results, research directed at biological control of Hawaiian infestations should focus on areas in the KwaZulu-Natal region in South Africa where host-specific natural enemies are most likely to be found. Our results show that phylogeographical analysis is a potential powerful and efficient tool to address questions relevant to invasion biology of plants.