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Arid environments are characterized by a patchy distribution of resources (soil nutrients and water availability) which often accrue under or around shrubs. These so-called ’fertile islands’ have high levels of organic matter, nutrients, and mycorrhiza inocula. Interactions between arbuscular mycorrhizal fungi (AMF) communities and plants, as well as their distribution, are poorly known in these ecosystems, although elsewhere their relevance in ecosystem function is well known. Here, we characterized the AMF community colonizing roots of two plant species, Ballota hirsuta and Lobularia maritima, growing in both patches and open areas. We found differences between AMF genetic composition of communities associated with the two plant species, suggesting specificity. The similarity of AMF colonizing roots of the same plant species was higher in open areas than in patches, while there were differences in AMF genetic richness and diversity between target species in open areas. These data provide new information on the specificity of AMF-plant interactions in patchy environments, and suggest a control of AMF on plant population and community dynamics in arid ecosystems. (C) 2011 Elsevier B.V. All rights reserved.