Understanding the relative abundance of species in plant communities is an unsolved problem. Mechanisms such as competition, resource partitioning, dispersal ability and predation tolerance do not adequately explain relative abundance under field conditions. Recent work suggests that interactions between plants and soil microbes is important. Here I show that such interaction explains a significant proportion of the variance in the relative abundance of species in plant communities. Rare plants exhibited a relative decrease in growth on 'home' soil in which pathogens had had a chance to accumulate, whereas invasive plants benefited from interactions with mycorrhizal fungi. Some plant species accumulate pathogens quickly and maintain low densities as a result of the accumulation of species-specific pathogens, whereas others accumulate species-specific pathogens more slowly and do not experience negative feedback until plant densities reach high levels. These results indicate that plants have different abilities to influence their abundance by changing the structure of their soil communities, and that this is an important regulator of plant community structure.