In fragmented landscapes, many species live in a patchy environment in which their local populations frequently become extinct and “empty” sites are recolonised through dispersal from other populations. The process of local extinction is often driven by the interactions between different trophic levels (e.g. herbivore-parasitoid interactions). The multi trophic system we studied consists of the patchy distributed plant Senecio jacobaea, its specialist herbivore, Tyria jacobaeae, the specialist parasitoid, Cotesia popularis, and the hyperparasitoid, Mesochorus facialis. The spatial scale we looked at ranged from several meters up to several hundred kilometres. We examined the effect of the spatial structure of the host metapopulations on the genetic diversity and structure of the herbivore and both parasitoids, using molecular fingerprinting techniques (AFLP, RAF). All three species displayed significant genetic differentiation among plant patches sampled. C. popularis displayed, as expected, a higher differentiation among the patches sampled than did its host T. jacobaeae. The hyperparasitoid, M. facialis, unexpectedly showed the lowest differentiation among its patches of all three species. A significant positive correlation between the genetic and the geographic distance (isolation by distance) was found for the samples of the herbivore and the hyperparasitoid, but not for the parasitoid. The genetic diversity within the patches of the three species was not correlated with the connectivity of the patch. T. jacobaeae displayed significantly higher genetic diversity within plant patches situated in natural areas than within patches situated along roadsides or in industrial areas. The genetic diversity of C. popularis was significantly positively related to its patch size only, whereas for M. facialis none of the habitat characteristics was related to its genetic diversity. Our findings show that the species of the different levels experience different influences and pressures that define their genetic structures, despite the fact that they live in the same patchily distributed environment.