The diversity of arbuscular mycorrhizal fungi (AMF) in roots of two plant species (arar, Tetraclinis articulata and lavender, Lavandula multifida) that exist alone or co-occur in Moroccan Tetraclinis woodlands was characterized using molecular techniques. The interaction between the two plant species on their root AMF communities was also studied. We analysed the large subunit (LSU) ribosomal RNA gene amplified by nested PCR from a root DNA extract using AM fungal-specific primers. A total of 200 cloned fragments from five root bulk samples of the two plant species were analysed by restriction fragment length polymorphism (RFLP) and 30 of them were sequenced. Phylogenetic analyses demonstrated that these RFLP types correspond to eight phylotypes: five belonged to the Gigasporaceae and three to the Glomeraceae. The highest diversity was found in the roots of T. articulata alone, followed by the association T. articulata/L. multifida and, finally, L. multifida alone. Many AMF were shared between the two species, although a few of them had a preference for one or the other. In addition, PCA analysis showed clearly that the AMF community colonizing T. articulata differed significantly from that colonizing L. multifida. Our results reveal an impact of plant interactions on the AMF community.