This study determined the influence of soil nitrogen and phosphorus on the colonisation dynamics of arbuscular mycorrhizal fungi (AMF) and Dark Septate Endophytes (DSE) in plant species adapted to nutrient poor soils. Plant colonisation dynamics were investigated using a field experiment and a manipulative greenhouse experiment on Australian native seedlings. Tubestock of Poa labillardierei were transplanted into the field to large tracts of land of high and low nutrient availability, near Sydney, Australia, and root colonisation was determined from monthly plant collections over three months, between late austral autumn and through winter. In the greenhouse experiment, two native shrubs and one grass, respectively, Rhagodia candolleana, Dodonaea triquetra and P. labillardierei, were germinated from seeds and grown under a full factorial nitrogen and phosphorus fertilisation experiment for three months before root colonisation was determined. The selected study species were of varied mycotrophy. AMF colonisation in both experiments was lowest in plants from high nutrient treatments. Removal of either nitrogen or phosphorus from the fertiliser resulted in the same patterns of colonisation, with AMF being greater when either nutrient was removed. DSE colonisation was greatest in high nutrient soils. However, colonisation did not vary with nutrient treatments in the glasshouse experiment, suggesting that nitrogen and phosphorus minimally affect DSE colonisation. The difference in AMF and DSE colonisation patterns��demonstrates a distinction in how different fungal symbionts are affected by abiotic factors. Both nitrogen and phosphorus are important drivers of colonisation dynamics of AMF. The results indicate the potential for disparate controls of AMF and DSE root associations.