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The intercropping of grasses and legumes has been suggested as an alternative for ensuring pasture sustainability. However, few studies have focused on the impact of intercropping and shading on the soil microbiota in semi-arid regions. The goal of this study was to evaluate the effects of intercropping a grass, Cenchrus ciliaris, with a legume, Clitoria ternatea, under different levels of shading, on the C. ciliaris carbohydrate concentration and the arbuscular mycorrhizal fungal (AMF) community over time. Soil samples were collected at four sampling times: before intercropping (BI) and after 120, 165 and 210 days cultivation. Four levels of shading were tested: 0 (full sunlight), 26, 39 and 55%. In the intercropped system, mycorrhizal colonization was higher under lower shading levels after 120 and 165 days cultivation, but the number of glomerospores was higher under higher shading levels. After 165 days cultivation, the carbohydrate concentrations were higher under full sunlight. After 210 days cultivation, the reducing carbohydrate concentrations were higher in the intercropped system. Thirty-one AMF species were detected; Acaulospora and Glomus species were predominant compared with the remaining genera. This study showed that AMF community composition was relatively similar between shading and intercropping by multidimensional scaling (MDS) and PERMANOVA analysis, and it was observed only sampling time effect on the AMF community. The Shannon diversity index showed a reduction in AMF diversity from 210 days of cultivation and an increase in the AMF species richness over time. It was concluded that pastures of C ciliaris under shading and intercropping with C ternatea did not modify the AMF community composition. However, the results suggest that intercropping of these plant species may result in AMF species selection over time. (C) 2016 Elsevier B.V. All rights reserved.