Introduction The association between arbuscular mycorrhizal fungi (AMF) and root plants occurs over a broad ecological range, from aquatic to desert environments [1]. The global distribution, beneficial effects on plant growth and ecological importance of AMF has been well documented. However, knowledge of their community structure is scarce. In recent years, more information has been reported regarding the functional role of AMF in ecosystems [2]. Studies under mesocosm, field plot and natural conditions suggest that belowground diversity of AMF may influence vascular plant community structure and composition [3, 4]. In order to understand factors structuring plant communities, more information is needed about the natural distribution patterns of AMF. It is thus necessary to identify the fungi associated with natural ecosystems and agroecosystems. Only about 150 AMF species have been formally described [5]. Establishment of phylogenetic relations, identification and classifications are based on morphological features of the asexually produced propagules (spores, sporocarps). In the absence of spores, the intraradical structures allow identification to the family level at the most [6]. However, in most cases the identification of AMF is generally difficult or almost impossible [7].