Polyphagous insect herbivores experience different selection pressures on their various host plant species. How this affects population divergence and speciation may be influenced by the bacterial endosymbionts that many harbor. Here, we study the population structure and symbiont community of the pea aphid (Acyrthosiphon pisum), which feeds on a range of legume species and is known to form genetically differentiated host-adapted populations. Aphids were collected from eight legume genera in England and Germany. Extensive host plant-associated differentiation was observed with this collection of pea aphids comprising nine genetic clusters, each of which could be associated with a specific food plant. Compared to host plant, geography contributed little to genetic differentiation. The genetic clusters were differentiated to varying degrees, but this did not correlate with their degree of divergence in host use. We surveyed the pea aphid clones for the presence of six facultative (secondary) bacterial endosymbionts and found they were non-randomly distributed across the aphid genetic clusters and this distribution was similar in the two countries. Aphid clones on average carried 1.4 species of secondary symbiont with those associated with Lathyrus having significantly fewer. The results are interpreted in the light of the evolution of specialization and ecological speciation.