Hydrogen is considered as a fuel for the ‘‘future’’ because it has the highest energy density of 3042 cal/m3. Especially the production of biological hydrogen is promising as it can be obtained from a variety of organic feedstocks. Anaerobic co-digestion has been attracting strong interest due to its potential to improve the buffer capacity, the nutrient balance, the carbon/nitrogen (C/N) ratio and the macro and micronutrients concentration. A balanced C/N ratio allows enhancing the buffer capacity of the system. Additionally, the co-digestion process also reduces the possibility of inhibitory effects, which, in turn, increases the yield of biohydrogen production. On the other hand, the knowledge of the process in biohydrogen reactors has to be improved especially for industrial biohydrogen production applications from complex feedstocks. . For instance, the analysis of the microbial community structure is essential for determining how the activity is affected inside the bioreactors. Thus, the knowledge about the dynamics of the microbial community structure and activity is essential for a successful planning of the biogas process, monitoring its parameters and for reaching the main goal of process stability and maximum biohydrogen yield.