Biologists have long been interested in the maintenance of biodiversity at both the genetic and species level, but have traditionally studied the two levels in isolation. However, diversity at one level may depend critically on the diversity of the other. Previously, I showed that genetic variation in allelochemical concentration in Brassica nigra mediates coexistence between B. nigra and its interspecific competitors, and that the diversity of competing species allows for the maintenance of genetic variation in the trait. Here I show that this result is driven primarily by an indirect effect mediated through changes in mycorrhizal fungal mutualists in soils dominated by high or low glucosinolate B. nigra genotypes. A greenhouse experiment found that the observed field patterns could be reproduced using only the soils from under the various communities (high or low glucosinolate B. nigra or diverse multi-species patches), but not when arbuscular mycorrhizal fungi were removed from these soils. Soil pathogens may also play a role in determining the fitness of the B. nigra genotypes. Thus understanding, and conserving, species diversity may require an understanding of genetic diversity, and vice versa.