In recent years bioethanol has encompassed worldwide interest as a non-conventional bioenergy source. This fact has driven several bioethanol industries to produce more ethanol on a large scale via cost effective methods. However in the process of scaling up ethanol production bacterial contamination is becoming one of the more challenging problems facing the bioethanol industry. There are several traditional microbiological methods available to detect and subsequently limit these bacterial contaminants. These methods are time consuming, laborious and can be less sensitive. Consequently, it is necessary to find novel sensitive and economic detection methods to eradicate the contaminants long before they disrupt ethanol production. Molecular methods that can detect the contaminants even at very low numbers at any given stage would help in the design of more cost effective eradication strategies and better targeted antimicrobial treatments. Application of rapid molecular detection approaches have the potential to provide much more sensitive and rapid means to not only detect but quantitate microbial contaminants long before they become problematic to overall bioethanol formation. (C) 2009 Elsevier Ltd. All rights reserved.