Molecular methods, both qualitative and quantitative, have become important in hydrogen-fermenting community analyses to reveal the complexity of the community and to monitor the changes and interactions in the communities during bioprocesses. This review presents a survey of the methods used to characterize hydrogen-fermenting mixed cultures. Each method has its pros and cons and, therefore, several methods are often used in combinations to provide the best results. The methods used are mainly PCR based targeting the 16S rRNA gene, but also other methods and targets, such as the hydrogenase genes or their transcripts, are well represented. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.