Fertile islands' or 'resource islands' are considered to be a featured pattern in desert ecosystems. Water and nutrient contents are found to be higher in under- than inter-shrub soils. One general idea is that soil water and nutrients have a close correlation with microbes. However, it remains controversial on whether the spatial distribution of soil microbes around shrubs is determined by soil water and nutrients of fertile islands. In addition, different microbial groups, such as fungi, bacteria, Gram-positive and Gram-negative bacteria, have distinct sensitivity or tolerance to the changes of soil water and nutrients. How these microbes distribute around shrubs and their relations with soil water and nutrients calls for further study. In the current study, under- and inter-shrub soils of Haloxylon ammodendron(height 200-210 cm, basal diameter 9-10 cm and crown width 200 × 200 cm), a dominant species in desert ecosystems of Gurbantunggut Desert, were studied. Soil samples were collected in circles with radii of 5, 40, 100 and 200 cm respectively from tree base in horizontal directions, and from depths of 0-20 cm. The sampling points of 5, 40, 100 and 200 cm represent the vicinity of tree base, the center of canopy, the edge of canopy and barren interspaces of shrubs, respectively. Soil samples from four directions, with angles between the adjacent directions at 90°, were mixed to obtain one composted sample. By analyzing changes in soil microbial biomass, diversity and community composition with changes of soil water and nutrients outward from tree base, the features of spatial distribution of soil microbes around shrubs was revealed. Microbial biomass, abundance and community composition were examined using phospholipid fatty acids. Redundancy analysis (RDA) was conducted to assess the correlations between soil properties and microbes. With the decreasing of soil water and nutrient content from the vicinity of tree base to interspaces of shrubs, total microbial biomass and diversity, as well as the biomass of different microbial groups, decreased gradually, indicating an increase of soil microbes inward from interspaces of shrubs. In addition, for the microbial composition in the soil, the biomass of different microbial groups had different reduction rate outward from tree base. For example, from the vicinity of tree base (i.e. 5 cm) to interspaces (i.e. 200 cm), the biomass of fungi, bacteria, Gram-positive and Gram-negative bacteria reduced 50.25%、84.06%、82.70%、92.57%, respectively. RDA results also showed that soil water, available nitrogen and organic carbon had a stronger correlation with bacteria comparing to fungi, and Gram-negative bacteria also correlated stronger than Gram-positive bacteria. This demonstrated that inward from interspaces, the increases of bacteria was more significant than fungi, and that of Gram-negative bacteria was more significant than Gram-positive bacteria. Our study suggested that soil microbes tended to distribute in soil resource-rich areas under the shrub canopy in resource-poor desert ecosystems. The spatial distribution of soil microbes was influenced more directly by soil properties than microclimate factors. Furthermore, the spatial distribution of soil microbes was not only determined by soil resource abundance, but also by the tolerance or sensitivity of different groups of microbes to environmental variations.