Today, the environmental awareness is leading to the recovery of the solid organic waste and the use of fossil fuels. Methanisation, or anaerobic digestion, is a solution. This process is the transformation of organic matter by bacteria in the absence of oxygen. It allows both the treatment of organic waste and provides two main products biogas and digestate. Digestate is an improved fertilizer that can be used by spreading or composting. Biogas can be used to produce heat or electricity. Biogas production is currently supported by governments of developed countries. In France, the number of installations is gradually increasing (Club Biogaz ATEE, 2011). However, waste used as raw material can potentially be rich in microorganisms. Currently, some questions arise about the potential spread of micro-organisms by this type of process. Among the among the dispersal pathways, the airborne mode of spread is often poorly explored. During the anaerobic process, a few phases seem to be able to cause the aerosolization of microorganisms, for example, the stock of raw materials or digestate handling. In this context, the EMAMET project was realised to provide data on atmospheric emissions from these processes (Bayle et al, 2016). The objectives of this study are to enumerate and describe the airborne microbial community on anaerobic digestor site caracterized by molecular approach. On a quarterly basis, over a one-year period, of the anaerobic digestion of waste water activated sludge has been monitored. For each campaign, four sampling locations have been investigated; the storage area for raw materials, the raw material preparation area, the digestion reactor and the phase separation zone of the digestate. A fifth simple, an outdoor control sampling point was also included.