Food webs typically quantify interactions between species, whereas evolution operates through the success of alleles within populations of a single species. To bridge this gap, we quantify genotypic interaction networks among individuals of a single specialized parasitoid species and its obligate to cyclically parthenogenetic aphid host along a climatic gradient. As a case study for the kinds of questions genotype food webs could be used to answer, we show that genetically similar parasitoids became more likely to attack genetically similar hosts in warmer sites (i.e. there was network-wide congruence between the within-species shared allelic distance of the parasitoid and that of its host). Narrowing of host-genotype-niche breadth by parasitoids could reduce resilience of the network to changes in host genetic structure or invasion by novel host genotypes and inhibit biological control. Thus, our approach can be easily used to detect changes to sub-species-level food webs, which may have important ecological and evolutionary implications, such as promoting host-race specialization or the accelerated loss of functional diversity following extinctions of closely related genotypes.