Bioethanol continues to be offered as a viable solution for complex problems ranging from global warming and national energy security to local economic development. Fuel bioethanol burns cleaner than gasoline, is derived from renewable agricultural products, and creates local jobs and income. In December 2007, President Bush signed into law the Energy Independence and Security Act, which increased the renewable fuel standard that was mandated under energy Policy Act of 2005 to 36 billion gallons by 2022.In order to achieve this goal, ethanol production would need to be generated primarily from corn and cellulosic materials. Bioethanol producers are currently involved in variety of technological innovations to reduce energy consumption and production costs, increased efficiency and reduced emissions using the best available control technologies. However, industrial ethanol fermentation is a non-sterile process and contaminant microorganisms can lead to a decrease in industrial productivity and significant economic loss. Currently, bioethanol industries use different antimicrobials including antibiotics to control the contaminants in the fermentors. The emergence of antibiotic resistance among contaminant bacteria in bioethanol fermentors warrants the need for alternative antimicrobials to retain bioethanol production at a profitable level. In addition more and more ethanol producers are seeking to generate distillers grains that can be labeled antibiotic free to be sold in international markets where some restrictions are already in place for reducing and/or eliminating antibiotics usage in animal feed. This review examines the contamination problems, various intervention methods, emergence of antibiotic resistance in contaminant bacteria, and potential alternative options to elucidate antimicrobial products from various natural sources. In particular, emphasis has been given for natural antibacterial products from plant derived products to suggest a new research avenue for the search of new, non-conventional antimicrobial agents to control the contamination problem in the fuel bioethanol industries. (C) 2010 Elsevier Ltd. All rights reserved.