Arbuscular mycorrhizal (AM) fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. Based on recent studies using high throughput molecular methods and their findings, I will give an overview on the factors driving AM fungal community assembly at different scales. By synthesizing these findings, I will show how modern coexistence and assembly theory can be adapted to arbuscular mycorrhizal fungi and that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. This conceptual framework developed for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.