Biological soil crusts (BSCs) are an important source of organic carbon, and affect a range of ecosystem functions in arid and semiarid environments. Yet the impact of grazing disturbance on crust properties and soil CO(2) efflux remain poorly studied, particularly in African ecosystems. The effects of burial under wind-blown sand, disaggregation and removal of BSCs on seasonal variations in soil CO(2) efflux, soil organic carbon, chlorophyll a and scytonemin were investigated at two sites in the Kalahari of southern Botswana. Field experiments were employed to isolate CO(2) efflux originating from BSCs in order to estimate the C exchange within the crust. Organic carbon was not evenly distributed through the soil profile but concentrated in the BSC. Soil CO(2) efflux was higher in Kalahari Sand than in calcrete soils, but rates varied significantly with seasonal changes in moisture and temperature. BSCs at both sites were a small net sink of C to the soil. Soil CO(2) efflux was significantly higher in sand soils where the BSC was removed, and on calcrete where the BSC was buried under sand. The BSC removal and burial under sand also significantly reduced chlorophyll a, organic carbon and scytonemin. Disaggregation of the soil crust, however, led to increases in chlorophyll a and organic carbon. The data confirm the importance of BSCs for C cycling in drylands and indicate intensive grazing, which destroys BSCs through trampling and burial, will adversely affect C sequestration and storage. Managed grazing, where soil surfaces are only lightly disturbed, would help maintain a positive carbon balance in African drylands.