Within an ecological community, interactions between species in a community occur directly, through physical contact, and indirectly, via other species or through abiotic environmental modification. Genetic variation within a species has the ability to alter the outcome of interactions between species. In other words, the specific genotypes of the interacting individuals are important for the outcome of the interaction. In this thesis, I begin by showing that indirect interactions between a soil rhizobacteria (Pseudomonas aeruginosa) and a parasitoid wasp (Aphidius rhopalosiphum) are mediated by genotypic interactions between the two linking species, aphids (Sitobion avenae) and barley (Hordeum vulgare). This means that the magnitude and direction of the indirect effect of rhizobacteria (presence/absence) on the wing size of the parasitoid wasp was different, depending on the combination of interacting aphid and barley genotypes. If such interactions were to have an evolutionary effect, there would need to be non-random association between the aphid and barley genotypes. In the next chapter, I demonstrated that different aphid genotypes actively choose (no effect on reproductive rate) to colonize particular barley genotypes. I then showed that host preference of an aphid genotype could be altered by the presence, and sometimes genotypic identity, of another competing aphid genotype. I confirmed that these interactions were indirect, via the plant, by showing that aphid growth rate can be reduced when a plant is pre-conditioned with a different aphid genotype. Further investigation, using microarrays, showed that the different aphid genotypes induced differential gene expression in a single barley genotype. Many of these sequences belonged to known plant defense pathways and suggest a possible mechanism for the observed genotypic interactions between aphid and barley. In order to further understand the influence of within-species genetic variation on species interactions there is a need to consider these interactions in a natural system. I therefore investigated the influence of genetic variation within a single tree species on the associated plant and invertebrate communities in a complex, natural tropical ecosystem. I found that more closely related trees were host to more similar communities of epiphytic plants, leaf litter invertebrates around the base of the tree and trunk-dwelling invertebrates. This shows that even in a highly diverse, naturally occurring ecosystem the effect of genetic variation within a species can be an important factor for the structure of associated communities of both plants and animals.Research on the influence of within-species genetic variation on species interactions at a community level has wide applications for understanding how communities and ecosystems function, which can benefit agriculture, disease management and conservation practices.