Hydrogen production by dark fermentation is one promising technology. However, there are challenges in improving the performance and efficiency of the process. The important factors that must be considered to obtain a suitable process are the source of the inoculum and its pre-treatment, types of substrates, the reactor configurations and the hydrogen partial pressure. Furthermore, to obtain high-quality hydrogen, it is necessary to integrate an effective separation procedure that is compatible with the intrinsic characteristics of a biological process. Recent studies have suggested that a stable and robust process could be established if there was an effective selection of a mixed microbial consortium with metabolic pathways directly targeted to high hydrogen yields. Additionally, the integration of membrane technology for the extraction and separation of the hydrogen produced has advantages for the upgrading step, because this technology could play an important role in reducing the negative effect of the hydrogen partial pressure. Using this technology, it has been possible to implement a production–purification system, the ‘hydrogen-extractive membrane bioreactor’. This configuration has great potential for direct applications, such as fuel cells, but studies of new membrane materials, module designs and reactor configurations are required to achieve higher separation efficiencies.