Arbuscular mycorrhizal fungi(AMF) are ancient,asexual,and obligate symbiotic endophytes which have not been cultured in vitro.So there is some limitation in the study of mycorrhizology.While the molecular technology based on DNA analysis could increase the detection sensitivity and specificity of AMF.rDNA sequence homology and variability can reveal the relationship between species and their evolution.Thus rDNA sequence analysis are widely used in the classification,identification,genetic,ecology and bio-diversity of AMF.This article summarizes the rDNA sequence analysis techniques and their application in phylogeny,molecular detection and community structure of AMF in different plant vegetation.