Microctonus aethiopoides Loan (Hymenoptera: Braconidae) was introduced from Morocco to Australia and New Zealand for biological control of the lucerne pest, Sitona discoideus. Previous research has indicated that M. aethiopoides intraspecific genetic variation is more strongly associated with weevil host species than geographic origin. Cytochrome c oxidase subunit 1 (COI) sequences from parasitoids dissected from weevils collected during a survey of lucerne-growing areas in Morocco allowed us to further test this hypothesis. As found previously, there were two strong clades in M. aethiopoides with no geographical basis to this structure. Earlier research suggested that intraspecific variability within M. aethiopoides was related to weevil host genus (Sitona vs. Hypera), and the analysis confirmed that one of the clades corresponded strongly with the host Sitona discoideus. The other clade, however, previously characterised by parasitoids from Hypera postica also included parasitoids dissected from Charagmus spp., which is a sister genus to Sitona. It is suggested that food plant associations of the host weevils might have had an influence on the evolutionary history of the parasitoid.