Hybridization is known to be involved in a number of evolutionary processes, including species formation, and the generation of novel defence characteristics in plants. The genus Senecio of the Asteraceae family is highly speciose and has historically demonstrated significant levels of interspecific hybridization. The evolution of novel chemical defence characteristics may have contributed to the success of Senecio hybrids. Chemical defence against pathogens and herbivores has been studied extensively in the model species Senecio jacobaea, which is thought to hybridize in nature with Senecio aquaticus. Here, we use amplified fragment length polymorphisms (AFLPs) and pyrrolizidine alkaloid (PA) composition to confirm that natural hybridization occurs between S. jacobaea and the closely related species S. aquaticus. AFLPs are also used to estimate the ancestry of hybrids. We also demonstrate that even highly back-crossed hybrids can possess a unique mixture of defence chemicals specific to each of the parental species. This hybrid system may therefore prove to be useful in further studies of the role of hybridization in the evolution of plant defence and resistance.