F. graminearum is an important pathogen that causes head blight of cereal crops as wheat and maize. It also produces the mycotoxins (as Deoxynivalenol=DON) which are toxic to the human and animals. During the off season the pathogen survives in the soil, on weeds and in crop residues. A 24 weeks study was conducted in controlled conditions (microcosms of natural soil, 17 °C, 80% WHC) to test whether the presence of DON in the wheat crop residues gives competitive advantage to F. graminearum over the other soil microflora and fauna to survive and develop a primary inoculum during the decomposition process. This study was carried out in the presence of the whole soil biota (i.e. fungi, bacteria, protozoa, nematodes and earthworms). In this experimental approach, wheat straw was inoculated with F. graminearum. The latter was placed on the soil surface or incorporated into the natural soil. This experiment was conducted with (1mg DON/kg soil-straw mixture) and without DON. The molecular biomass of fungi, bacteria and F. graminearum was determined by qPCR (real time polymerase chain reaction). The changes in the community structure of fungi, bacteria, protozoa and nematodes were determined by T-RFLP (terminal restriction fragment length polymorphism). The results suggested that DON in wheat straw showed an impact on part of the biotic components of the soil but the impact depended on the communities and on the location of the wheat residues.