Species diversity of consumers is known to promote high attack rates when species differ in their traits and the resources they use. Yet, despite considerable work on the role of species diversity, we lack information on how genetic diversity at different trophic levels affects rates of ecosystem processes such as trophic interactions. Here, we assess whether the available genetic diversity in three trophic levels influences parasitism rates, both within and across generations. We used experimental population bottlenecks to create a gradient of decreasing genetic diversity of hosts and parasitoids, and measured rates of parasitism, host resistance to parasitism, and host survival over 11 host generations. Less-inbred parasitoid populations exerted higher parasitism rates (analogous to known effects of species diversity), however, this effect became weaker over time. We conclude that genetic diversity can have short-term ecological impacts in trophic systems, which can be altered in the long term by evolutionary processes.