To investigate the community diversify of arbuscular mycorrhizal fungi(AMF) of Flemingia macrophylla and Flemingia lineata.Methods:The nested-PCR, cloning, RFLP analyzing and sequencing techniques were used.Results:A total of 558 clones containing 18S rRNA genes from AMF were obtained.After RFLP analysis, 83 different RFLP types were obtained, which can be divided into 23 Operational Taxonomic Units (OTUs) by DNA sequence analysis.They belonged to 5 subjects, and Glomeraceae was the dominant group.After they were compared in MaarjAM database, 23 OTUs could be identified as 18 molecular virtual taxon, scattered in 13 different habitats.By statistical analysis, AMF communities were significantly different between F.macrophylla and F.lineata roots, the difference was statistically significant (P<0.001).Conclusion:Compared with the difference of AMF community in F.macrophylla and F.lineata roots, combining with the distribution features of AMF species in ecosystem, valuable environmental indicator data to choose site for the Flemingia plantation is provided.