More knowledge of community composition of arbuscular mycorrhizal (AM) fungi in ecosystems in relation to habitat type and land use intensity is needed. We studied AMF in 106 soil samples from pristine natural forests and a gradient of disturbance including semi-natural and intensively managed pastures of Terceira, Azores. Altogether, 42 spore morphotypes were detected from eight AMF families, revealing different fungal community structures among the three land use types. Spore density was highest in native forests and lowest in intensively managed pastures, but fungal richness was highest in semi-natural pastures and lowest in native forests. No significant difference occurred between intensively managed pastures and native forests. Members of Acaulosporaceae and Glomeraceae were dominant in native forests, while fungi from Gigasporaceae and Claroideoglomeraceae were most abundant in semi-natural and intensively managed pastures respectively, indicating family-based ecological preferences. Rarefaction analysis revealed that pastures supported more diverse AMF communities than native forests, because in high elevation pristine forests, a few rare species dominate. It is therefore likely that more species would be found with increasing survey effort. Further research is needed to clarify the influence of land use type on AMF diversity and distribution in remote islands, and the role of native AMF on soil ecosystem processes and the spread of exotic plants.