Globally, soil acidity is a restrictive condition for agricultural production in a large surface. The aim of this study was to assess arbuscular mycorrhizal fungi (AMF) diversity in cereal species roots exposed to aluminum (Al) phytotoxic level at different plant phenological stages. A microcosm experiment was conducted in a soil-less system. AMF communities were analyzed in root samples by using PCR-DGGE. Phenological stage has a significant effect on the diversity indices. Simpson diversity index indicated a significant dominance of some AMF operational taxonomic units (OTUs), which were present in higher proportion, presumably displaying functional roles influencing physiological processes within host plant cereal growing under acidic conditions. In addition, AMF-OTUs communities' profiles showed a clustering trend related to Al presence. The present study suggests that AMF diversity based on OTUs analyses obtained from DGGE profiles depends on cereal plant phenological stage and Al supply, which seems to be a relevant AMF trait and it would be used for developing management strategies for acidic soils. However, more studies are needed related to Al effect on AMF communities of cereal species roots and AMF dynamics under cultivation conditions through the use of metagenomic techniques.