BACKGROUND: Recently it has been proposed that the genetic diversity of foundation species influences the structure and function of the community by creating locally stable conditions for other species and modulating ecosystem dynamics. Oak species are an ideal system to test this hypothesis because many of them have a wide geographical distribution, and they are dominant elements of the forest canopy. In this study we explored the response of canopy arthropod community structure (diversity and biomass) to the level of genetic diversity of Quercus crassipes and Q. rugosa, two important canopy species. Also, we examined the effect of oak species and locality on some community structure parameters (diversity, biomass, rare species, and richness of arthropod fauna) of canopy arthropods. In total, 160 canopies were fogged in four localities at the Mexican Valley (ten trees per species per locality per season) RESULTS: Q. crassipes registered the highest number of rare species, diversity index, biomass, and richness in comparison with Q. rugosa. We found a positive and significant relationship between genetic diversity parameters and canopy arthropod diversity. However, canopy arthropod biomass registered an inverse pattern. Our results support the hypothesis that the genetic diversity of the host-plant species influences the assemblage of the canopy arthropod community CONCLUSIONS: The pattern found in our study provides a powerful tool when trying to predict the effects of the genetic diversity of the host-plant species on different community structure parameters, which permits assignment of a new conservation status to foundation species based on their genetic diversity.