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Despite the evident importance of arbuscular mycorrhizal fungi associated with the root system of plants inhabiting desert regions, the distribution and activity of arbuscular mycorrhizal fungi in desert ecosystems is not well known. In this study, the spatial distribution and colonization of arbuscular mycorrhizal fungi were investigated in a field study in the Negev Desert of Israel. Soil samples from depths of 0-10, 10-20, 20-30, 30-40, and 40-50 cm were collected under the canopies of Zygophyllum dumosum, Hammada scoparia, Artemisia herba-alba, and Atriplex halimus. Spore density and association of vesicular root system with arbuscular mycorrhizal structure groups such as vesicles, arbuscules, and hyphae were used to assess and compare the responses of arbuscular mycorrhizal fungi to plant cover and their abiotic environment. Different plant cover significantly affected arbuscular mycorrhizal fungal colonization and spore density. Higher spore density tended to be correlated with higher arbuscular mycorrhizal colonization under A. herba-alba and A. halimus, and vice versa for Z. dumosum and H. scoparia. At the tested soil depths, the highest arbuscular mycorrhizal colonization at the 20-30 cm depth did not coincide with higher spore density at the 10-20 cm depth. Sampling depth had a significant effect on spore density and the percentage of total arbuscular colonization. Spore density was positively correlated with vesicular colonization and negatively correlated with arbuscular colonization. Soil total soluble N exhibited a negative effect on spore density, while soil water content and organic matter content did not exhibit a significant correlation with arbuscular mycorrhizal fungal colonization and spore density.