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The influence of the shrub canopy on the spatial distribution of above and below ground arthropod communities in desertified ecosystems is largely unknown. Using the shrubs Hedysarum scoparium (H. scoparium) and Artemisia ordosica (A. ordosica) as model systems, the above and belowground arthropod communities were sampled by using pitfall trapping and handsorting, in order to examine the linkage between above and belowground arthropods across shrub microhabitats. Different profile layers harboured mostly distinct arthropod taxon and trophic groups that preferred specific microhabitats. Even the common taxa, including the Carabidae and Formicidae families, were found to have different abundance distributions in above and belowground soil layers across shrub microhabitats. Total abundance distribution was found to differ, while taxon-richness and Shannon-index distributions were similar in above and belowground parts across the shrub microhabitats. Markedly higher taxon-richness and Shannon-index values were found beneath the shrub canopy compared to the open spaces, particularly beneath the A. ordosica shrub canopy. The abundance distribution in above and below ground arthropod communities were affected by the shrub microhabitats along vertical and horizontal axes more than the richness and diversity of these communities. The A. ordosica shrub canopy (compared with the H. scoparium shrub) was found to have greater ecological implications on the spatial distribution of the arthropod communities. All these findings were expected to be helpful for the conservation of biodiversity, shrub plantation management, and desertification control.