There is currently a high level of interest in renewable energy resources, especially biofuel (bioethanol). The raw material to ethanol fermentation could be not only edible plantsbut also industrial and community wastes. Using such materials is economically and environmentally profitable. However; exposures to risk of high microbial contamination which can lead to significant limitation of ethanol production. Therefore, recognition and reduction of microbial contamination, as well as prevention of such infections are essential and need deeper understanding.