Patchy desert shrubs magnify the horizontal heterogeneities of carbon source and nutrient availability in an arid ecosystem, significantly affecting the abundance and activity of the soil microbial community. Since each shrub species develops special ecophysiological adaptations to the extreme harsh desert environments, previous studies elucidated that the effects of perennial shrubs on microbial diversity are unequal. The aim of the present study, conducted in the Negev Desert, Israel, was to illustrate the vertical changes of soil microbial community functionality in the root zone of perennial shrubs. Soil samples were collected from the 0-50 cm depth at 10-cm intervals under the canopy of Zygophyllum dumosum, Hammada scoparia, and from the open spaces between them, in the wet and dry seasons. Soil moisture and organic matter exhibited a significant (P < 0.001) plant and depth dependence. The mean basal respiration rates and microbial biomass in soils collected beneath perennial shrubs were relatively higher than the control during the wet season, however, a contrasting trend was observed at some soil depths during the dry season. Relatively high abundance and activity of aromatic and carboxylic acid utilizers were observed in the vicinity of perennial shrubs, and the values recorded during the dry season were generally higher than the corresponding values during the wet season. In addition, a "mirror effect" in vertical changes of the community-level physiological profile was observed between Z. dumosum and H. scoparia. This study demonstrated the stratification of the functional aspects in soils under the canopy of perennial shrubs, thus indicating that the scattered distribution of vegetation not only causes horizontal heterogeneities of the microbial community in an arid system, but also that the ecophysiological adaptations developed by xerophytes regulate the abundance and saprotrophic functionality of microorganisms in the root zone.