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Shrub presence has an important effect on the structuring of ground beetles in desert ecosystems. In this study, in order to determine how shrubs and different species influence ground beetle assemblages in a sandy desert scrubland dominated by two different shrub species, namely Calligonum mongolicum and Nitraria sphaerocarpa, we sampled the ground beetles using pitfall traps during spring, summer and autumn in 2012. At the community level, the activity density of the ground beetles was shown to be significantly higher under shrubs than in intershrub bare habitats in spring; but an opposite pattern occurred in autumn, suggesting the presence of season-specific shrub effects on the activity density of the ground beetles. Meanwhile, at the trophic group level, the activity density and species richness of predators were significantly greater under shrubs than in intershrub bare habitats in spring, whereas an opposite trend occurred on the activity density in autumn. N. sphaerocarpa shrubs had a positive effect on the activity density of herbivores in the three seasons, and C. mongolicum shrubs had a positive effect on the activity density of detritivores in spring and autumn. At the species level, more Microdera sp. was captured under shrubs than in intershrub bare habitats in spring. During the same time, we also found that C. mongolicum shrubs had a positive effect on Blaps gobiensis in spring, Carabus sp. in autumn, and Tentyria sp. in spring and autumn, and N. sphaerocarpa shrubs had a positive effect on Cyphogenia chinensis, Sternoplax setosa in spring and summer, and Curculionidae sp. 1 in summer and autumn. The study results suggest that shrub presence, shrub species and season variation are important factors for ground beetle assemblages in this desert ecosystem, but the responses of beetles differed among trophic and taxonomic levels.