The influence of wild fires on microbial community structure, soil organic matter, sulphur oxidising and nitrifying microbial populations in the floodplains of the Okavango Delta of Botswana was assessed. Microbial community structure was assessed by phospholipids ester-linked fatty acids (PLFA) quantification while microbial sulphur oxidisers were assessed by Most Probable Number (MPN). Community structure assessment showed that burning shifted the microbial community structure from single cellular bacteria being the dominant groups to filamentous fungi and actinomycetes being the most dominant groups. Generally burning increased the fungal component (18:2 omega 6) matrix from 3.40 to 8.35 while the actinomycetes and sulphur reducing bacterial (10 Me 16:0) component also increased from 1.02 to 1.70 mostly in the floodplains. Generally, the organic matter content declined with burning. However, the influence of burning on soil pH was non conclusive. Soil microbial biomass carbon increased slightly after the fire. The number of heterotrophic and nitrite-oxidizing and sulphur reducing bacteria increased. Overall, these results indicate that burning significantly alters the microbial community structure as large above ground losses of nutrients during and after burning often results in low quantities of nutrients released into the soil.