The holoparasitic angiosperm Orobanche minor parasitizes a diverse range of flowering plants from at least 16 orders in both the monocots and eudicots. However, populations of O. minor show host specificity at a local level. Our previous work identified the potential for host specificity to act as a catalyst for genetic divergence among populations of O. minor. Here we have extended this investigation by sampling populations from multiple hosts, across a broad geographic range. Sequence characterised amplified region (SCAR) data identified an exotic host-generalist lineage and a native host-specialist lineage of O. minor, suggesting genetic structure in this species is defined by both host specificity and geography. In addition, host-range overlap, discordant tree topologies, and cryptic morphology indicate the presence of gene flow between alien races and endemic populations. Therefore, repeated introductions of alien races of O. minor from disparate sources leading to introgression with native populations, and cryptic race formation, seem to have contributed to the taxonomic confusion associated with this species. We speculate that radiations associated with broad host range and divergent host ecologies may have promoted the unusually wide geographic distribution and diversification of this species. Finally, evidence of multiple shifts to exotic hosts, coupled with the predicted northward shift in climatic suitability, identify the potential for range expansion in alien races of O. minor, which may threaten nationally scarce native taxa with genetic assimilation. Our phylogenetic analysis provides a framework for identifying host races in Orobanche with a view to setting conservation priorities.