Genetic variation in foundation tree species can strongly influence communities of trophic-dependent organisms, such as herbivorous insects, pollinators, and mycorrhizal fungi. However, the extent and manner in which this variation results in unexpected interactions that reach trophic-independent organisms remains poorly understood, even though these interactions are essential to understanding complex ecosystems. In pinyon–juniper woodland at Sunset Crater (Arizona, USA), we studied pinyon (Pinus edulis) that were either resistant or susceptible to stem-boring moths (Dioryctria albovittella). Moth herbivory alters the architecture of susceptible trees, thereby modifying the microhabitat beneath their crowns. We tested the hypothesis that this interaction between herbivore and tree genotype extends to affect trophic-independent communities of saxicolous (i.e., growing on rocks) lichens and bryophytes and vascular plants beneath their crowns. Under 30 pairs of moth-resistant and moth-susceptible trees, we estimated percent cover of lichens, bryophytes, and vascular plants. We also quantified the cover of leaf litter and rocks as well as light availability. Four major findings emerged. (1) Compared to moth-resistant trees, which exhibited monopodial architecture, the microhabitat under the shrub-like susceptible trees was 60% darker and had 21% more litter resulting in 68% less rock exposure. (2) Susceptible trees had 56% and 87% less cover, 42% and 80% less richness, and 38% and 92% less diversity of saxicolous and plant communities, respectively, compared to resistant trees. (3) Both saxicolous and plant species accumulated at a slower rate beneath susceptible trees, suggesting an environment that might inhibit colonization and/or growth. (4) Both saxicolous and plant communities were negatively affected by the habitat provided by susceptible trees. The results suggest that herbivory of moth-susceptible trees generated litter at high enough rates to reduce rock substrate availability, thereby suppressing the saxicolous communities. However, our results did not provide a causal pathway explaining the suppression of vascular plants. Nonetheless, the cascading effects of genetic variation in pinyon appear to extend beyond trophic-dependent moths to include trophic-independent saxicolous and vascular plant communities that are affected by specific tree–herbivore interactions that modify the local environment. We suggest that such genetically based interactions are common in nature and contribute to the evolution of complex communities.< Réduire