Mycorrhizal fungi, root-associated symbionts of the vast majority of terrestrial plant species, are an important model for the study of the ecology and evolution of symbioses. Despite this, we lack an understanding of what drives the distributions of mycorrhizal fungi beyond broad generalisations regarding their roles in particular biomes. Using information obtained from the Biomes of Australian Soil Environments (BASE) soil microbial diversity database (https://downloads.bioplatforms.com/base/), we mapped of the distributions of two functionally and phylogenetically divergent groups of mycorrhizal fungi: the arbuscular mycorrhizal (AM) fungi and the ectomycorrhizal (EM) fungi. We found that the relative abundances of ITS sequence reads and the richness of operational taxonomic units (OTUs) belonging to these two groups of mycorrhizal fungi were responsive to environmental conditions (e.g., vegetation type and soil fertility) in ways that were expected based on current knowledge. However, for both AM and EM fungi, betadiversity (turnover in OTU composition) among samples was extremely high suggesting a largely stochastic assembly process within these communities. To determine whether environmental filtering might be acting on specific traits associated with these fungi, we integrating information regarding spore traits (from the International Culture Collection of [Vesicular] Arbuscular Mycorrhizal Fungi – http://invam.wvu.edu/ - and from species descriptions in the literature) with species of AM fungi identified and observed in BASE and calculated community weighted means for each sample. As an example, we found evidence for soil fertility and moisture influencing mycorrhizal fungal community composition via selection on spore colouration, which may be linked to biochemical adaptations to these conditions. This study emphasises how integrating data generated from DNA-based environmental surveys with trait data obtained at the species level is a promising approach to generate mechanistic knowledge of fungal adaptations to Australian environments and can lead to predictions regarding their consequences for ecological and evolutionary interactions with their hosts.