Arbuscular mycorrhizal fungi (AMF) are soil microbes that colonize up to 90% of all land plants and offer benefits in the form of nutrient acquisition, water retention, and resistance to pathogens and pests. AMF diversity is thought to respond to a range of biotic and abiotic factors in soil management practices. This was studied in a multi-year wheat field trial incorporating variation in fertiliser application (N and P), tilling and crop rotation. The AMF diversity in each sample was analysed by PCR amplification with AMF-specific DNA primers that span the small sub-unit to the large sub-unit of the ribosomal RNA gene and the products were sequenced using Illumina MiSeq. These primers were chosen for this study because they provide greater coverage and depth of AMF sequences compared to traditional fungal primers. The AMF diversity of individual samples differed by treatment in fertiliser type and amount, tilled versus not-tilled, and previous crop rotations of canola or chickpea. Bioinformatic analyses showed a strong correlation between AMF diversity and field trial conditions, particularly between the AMF genus Funneliformis and rhizosphere samples with no fertiliser or tilled treatments, and grown in conjunction with chickpea during rotation years. This indicates that treatments have a strong influence on AMF species diversity in agricultural trials, which may be explained by the filling of niches dictated by functional traits at the AMF genus or species level. Further research on functional traits will elucidate how AMF can be strategically applied for reducing chemical inputs and water use in agriculture.