Arbuscular mycorrhizal fungi (AMF) are essential functional microbiology in natural ecosystems. It is very important to research community composition and di- versity of AMF for achieving sustainable development of ecosystems. The paper described several methods of researching the diversity of AMF, especially for molecular techniques, reviewed the application status of these methods in AMF research, and pointed out that the effective combination of morphological and molecular methods could better reveal the biodiversity and ecological functions of AMF in natural ecosystems.