The flea beetle Phyllotreta nemorum is an oligophagous species using crucifers as host plants. In Denmark two populations have been found which use Barbarea vulgaris ssp. arcuata (G-type) as a host plant, whereas this plant is unsuitable for the survival of the majority of P. nemorum. In the locations in which these two populations occur, alternative host plants are also present. The plants occur in patches, some of which contain a mixture of host plants. In this study of allozyme variation, genetic differentiation between P. nemorum using different host plants in patches in the two different localities was studied hierarchically to assess substructuring of the populations. Evidence was found for low, but significant, amounts of genetic differentiation between (sub)populations using spatially separated plant patches at a distance of ≈100 m to 1 km (θ = 0.009) and between localities ≈ 44 km apart (θ = 0.026), and there was an association between genetic differentiation and geographical distance. No genetic differentiation was found between beetles from different host plants with overlapping local distributions. No evidence was thus found for sympatric host race formation. The geographical distribution of genes enabling P. nemorum to use B. vulgaris as a host plant (100%‘resistant’ beetles in samples from B. vulgaris, but much fewer on patches containing only alternative host plants) contrasts with the relatively low amount of genetic differentiation at the neutral allozyme loci. This distribution of ‘resistant’ beetles (to B. vulgaris defence) is likely to be influenced by local differences in selection and asymmetric gene flow.