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Desert ecosystems are characterized by sparse vegetation that affects both abiotic parameters and soil biota along the soil profile. This study was conducted in 2010-2011 in a loess plain in the northern Negev Desert highlands, Israel, to test two main hypotheses: 1) the abundance and diversity of microarthropods would vary seasonally in the top 30-cm soil layer, but would be relatively stable at soil depths between 30 and 50 cm and 2) soil microarthropods would be more abundant in soils under shrubs with large litter accumulations than under shrubs with less litter or bare soil. Soil samples were collected each season from the 0-50 cm profile at 10-cm intervals under the canopies of Hammada scoparia and Zygophyllum, dumosum and from the bare interspaces between them. Soil moisture and soil organic carbon in the top 30-cm layers varied seasonally, but there was little variation in the soil layers deeper than 30 cm. Soil mites were most abundant in the top 30-cm soil layer in autumn and winter, with the highest number of families found in winter. There were no differences in soil microarthropod abundance attributable to the presence or absence of shrubs of either species. The microarthropod communities of the microhabitats studied consisted of Acari, Psocoptera, and Collembola. The Acari were mostly identified to the family level and were dominated by Oribatida (55%) and Prostigmata (41%) in all seasons and microhabitats, while the psocopterans were most abundant in summer. These results are opposite to those obtained in other studies in similar xeric environments. Moreover, our findings were not in line with our hypothesis that a better microhabitat played a major role in microarthropod community composition, diversity, and density.