Many Acacia species are known to improve soil fertility and yields of associated crops. Their capacity to form symbiotic associations with soil bacteria called Rhizobium and mycorrhizal fungi improves growth and mineral nutrition. Associated crops can take benefits of this by acquiring some N and organic matter (mainly through litter). Acacia species are therefore very important in arid and semi arid zones, where land degradation and deforestation induce soil fertility decline. Acacia Senegal is a species of major importance because it produces gum arable. This gum has very high economic value and it is an important source of cash income for farmers. Growth and vigour of the trees can be improved by inoculation by specific Rhizobium strains. This inoculation also has a positive effect on the production of gum Arabic. This study, conducted using soils from Senegal, Burkina Faso and Niger assesses the changes caused by the inoculation by Sinorhizob^um strains on bacterial and fungal communities from different periods : rainy and dry (gum production) seasons. Bacterial and fungal diversity are assessed by DGGE and Shannon indexes based statistical analysis. Results show different effects on microbial diversity, depending on countries. In Senegal, bacterial diversity is affected by inoculation, and bacterial and fungal diversities are increased in dry season. Bacterial diversity is increased in dry season in Niger as well, but there is no significant effect of both factors in Burkina Faso. More studies will be conducted by PCR-DGGE to target specific communities, which are involved in nitrogen cycle.