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. Previously studies on microbial population analysis at the initial stage of the co-digestion in batch system showed that Bifidobacterium had a predominance of 85.4 %, while hydrogen producing bacteria such as Klebsiella (9.1 %), Lactobacillus (0.97 %), Citrobacter (0.21 %), Enterobacter (0.27 %), and Clostridium (0.18 %) were less abundant at this culture period. The microbial community structure with the lactate and acetate production was correlated a hydrolytic stage, while butyrate production was correlated a hydrogenic stage. In this context, the co-digestion process of crude cheese whey (CCW) with fruit vegetable waste (FVW) for biohydrogen production was investigated in continuous systems, in stirred 1.8 L bioreactor at 37°C in two stages. At hydrolytic stage were carried out 55-batches at a C/N ratio of 21. While in hydrogenic stage, eight different conditions of hydraulic retention time (from 60 to 10 h) and organic loading rate (from 21.96 to 155.87 g COD/L d) were evaluated. The optimum hydraulic retention time and organic loading rate were 17.5 h and 80.02 g COD/L d, respectively. Under these conditions, the highest volumetric production hydrogen rate (VPHR) and hydrogen yield were 11.02 mmol H2/L h and 800 mL H2/COD, respectively. Additionally, the results demonstrated that the co-digestion of CCW with FVW improves the biohydrogen production due to a better nutrient balance and improvement of the system’s buffering capacity. Hence, the results obtained in this study increase the knowledge about the influence of mixing different substrates on the microbial community structure involved in the anaerobic co-digestion degradation of real feedstocks and provide valuable information to optimize the fermentation process. Finally, the characterization of microbial community structures should be also considered in the engineering context, as the understanding of the microbial community structure can provide information to analyze the anaerobic process under dynamic conditions and optimize the biohydrogen production process.