The hypothesis of the present study was that microbial communities would differentiate under Eucalyptus camaldulensis and that this influence will modify microbial functional diversity. A further hypothesis was that an enhancement of arbuscular mycorrhizal (AM) density (through controlled fungal inoculation) would minimize this exotic plant species effect through a well-developed mycelium network. Treatments consisted of control plants, pre-planting fertiliser application and AM inoculation. After 4 months of culture in autoclaved soil, E. camaldulensis seedlings were either harvested for growth measurement or transferred into containers filled with the same soil but not sterilized. Other containers were kept without E. camaldulensis seedlings. After 12 months, effects of fertilizer amendment and AM inoculation were measured on the growth of Eucalyptus seedlings and on soil microflora. The results clearly show that this plant species significantly modified soil microbial community. Both the community structure (assessed by DGGE profiles) and function (assessed by SIR responses including soil catabolic evenness) were significantly affected. The changes in the microbial structure and function were accompanied by disturbances in the composition of the herbaceous plant species layer. Hence, these results highlight the role of AM symbiosis in the processes involved in soil bio-functioning and plant coexistence.