Sequences of the nuclear rDNA ITS region were sampled from a natural population of an arbuscular mycorrhizal fungus, Acaulospora colossica. Genetic diversity was explored through three levels of sampling: within an individual (a single spore), between individuals of a single soil sample, and between individuals of different soil samples across a 36 m2 area. High levels of ITS sequence variation were discovered, and sequences from different spores and different soil samples were sometimes more similar than sequences of the same spore or soil sample. These results demonstrate a complex pattern of rDNA organization within a natural population of Glomalean fungi, and challenge ideas of individuality and collectivism in fungi.