In the Sahel two native shrubs (Piliostigma reticulatum and Guiera senegalensis) coexist in farmers’ fields but little information is available on microbial ecology and activities of their rhizospheres.  This could be important for understanding biogeochemical processes and functioning of agroecosystems of this semi-arid region.  For each species, in the rainy and dry seasons, soil was collected from the rhizosphere, bulk soil beneath the canopy, and from outside the shrub rhizosphere (>two meters) (0-10 cm depth). PLFA and DGGE analysis were used for microbial diversity and community structure analysis, along with key hydrolytic enzymes. Multivariate analysis of DGGE profiles showed that the bacterial community was primarily influenced by the rhizosphere where as the fungal structure was influenced by season. NMS analysis of PLFA community composition showed that spatial variability was more apparent than the temporal changes. The fungal biomarker (18:2 ω6c) as well as the actinomycete biomarker (10Me 18:0) strongly influenced the distribution of the microbial community between rhizosphere and non-rhizosphere soil.  Enzymes activities, β-glucosidase and chitinase activities were strongly correlated with the community composition. In summary the rhizosphere had had greater microbial diversity and activity regardless of season than bulk soil beneath or outside the shrub canopy.