The aim of this study was to investigate the impact of subterranean fungus-growing termites on the structure of soil microorganism communities. We tested whether termites significantly modify the abundance and structure of microbial communities within their below-ground nests (fungus-comb chambers) and whether these effects are species-specific. The investigations were carried out in a humid savanna reserve with material collected from the fungus-comb chamber walls of two widespread species differing in the mode of nest construction. Ancistrotermes builds diffuse and ephemeral nests while chambers of Odontotermes are mostly concentrated and occupy the same area for a comparatively much longer period of time then creating lenticular mounds. The soil properties (pH, texture and C, N content) and the microbial biomass were analysed and automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities. Our results illustrate that the nest structures created by termites offer a diverse range of physical and chemical environments that differ strongly from those present in the general soil mass. Odontotermes had strong effects on microbial properties at the scale of the fungus-comb chamber and at the scale of the lenticular mound. In the fungus-comb chambers, the microbial biomass is not affected by termites but the structure of microbial community is different from that in the control open savanna soil. In the lenticular mound, the microbial biomass is higher and the structure of bacterial community is distinct than that in the fungus-comb chambers. Ancistrotermes also strongly influenced the structure of soil bacterial and fungal communities in the open savanna. However, we did not find any significant modification of bacterial and fungal community structures in the lenticular mound. The impact of fungus-growing termites is, therefore, species-specific and varies depending on the study site (open savanna vs. lenticular mound).