The addition of a novel host plant to a phytophagous insect's diet may result in subsequent host-plant specialisation, and is believed to be a key cause for speciation in this trophic group. In northern Britain, the tephritid fly Tephritis conura has experienced a unique host-plant expansion, from the melancholy thistle Cirsium heterophyllum to the marsh thistle C. palustre. Here, we examine whether the incorporation of C. palustre in the repertoire of British T. conura flies has caused genetic divergence between populations infesting the old host and the novel host, and how British populations differ from populations infesting C. heterophyllum in continental Europe where C. palustre is not infested. No evidence for restricted gene flow among British C. palustre and C. heterophyllum flies was found. Significant differentiation between British and continental T. conura was found at only one allozyme locus, hexokinase, and caused by a new allele, Hex_95. Hexokinase is related to host-race formation in continental European flies infesting C. heterophyllum and C. oleraceum, and might be linked to loci determining host choice. Based on morphological and phenological data from previous studies, we suggest that T. conura in Britain has adapted to the novel host but that host-race formation is impeded by similar plant phenologies.