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Community composition of arbuscular mycorrhizal (AM) fungi was analyzed in the roots of five representative shrub species (Genista cinerea, Lavandula latifolia, Rosmarinus officinalis, Thymus mastichina and Thymus zygis) growing in a typical semi-arid Mediterranean ecosystem. Roots from a well-preserved area of the ecosystem were extracted from soil and analyzed by nested PCR, single strand conformation polymorphism and sequencing of the NS31-AM1 and NS8-ARCH1311 regions of the small subunit of the ribosomal DNA (SSU rDNA). Ten AM fungal phylotypes were identified; eight belonged to the Glomeraceae and two to the Diversisporaceae. Only two of the phylotypes clustered with sequences of morphologically defined species and a high dominance by one AM group (Glomus intraradices) was detected. Our diversity analyses revealed that the AM fungal communities of G. cinerea, L. latifolia and T. mastichina did not significantly differ while the AM fungal communities of R. officinalis and T. zygis were distant from this cluster and from each other. The highest diversity was found in the roots of T. zygis. Our data indicate that co-occurring plant species may house distinct communities of AM fungi. (C) 2012 Elsevier Ltd. All rights reserved.