Maternally inherited facultative endosymbiotic bacteria are common among insects, including many polyphagous insect herbivores. To investigate whether symbiont infection is structured by host plant in the polyphagous aphid Aphis craccivora Koch, pyrosequencing and diagnostic PCR were performed on 26 populations from two different host plants, alfalfa (Medicago sativa) or black locust (Robinia pseudoacacia). Results indicated that Aphis craccivora harbours distinctly different microbial communities in alfalfa versus locust. The facultative symbiont Hamiltonella was found only in aphids collected from alfalfa, and the facultative symbiont Arsenophonus was found only in aphids from locust. Hamiltonella is known to protect aphids against hymenopteran parasitoids, whereas the phenotypic effects of Arsenophonus in aphids are unknown. Correspondingly, a screen of the aphid samples for hymenopteran DNA indicated that Hamiltonella-bearing alfalfa populations of A. craccivora experienced lower parasitism than Arsenophonus-bearing locust populations. This study contributes to the growing body of evidence that correlative associations between bacterial endosymbionts and host plants may be a common phenomenon in polyphagous herbivores, and suggests that microbial symbionts have the potential to act as drivers for observed ecological differences among host-associated populations of polyphagous insects.