The main drawback of biohydrogen (bioH(2)) production by mono-digestion of vinasse and maize processing wastewaters (Nejayote) is related to high recalcitrance, unbalanced nutrients and unsuitable alkalinity. A novel co-digestion process of vinasse and Nejayote was proposed to overcome this problem. The effects of different vinasse/Nejayote ratios (i.e. 100/0, 80/20, 60/40, 40/60, 20/80 and 0/100 w/w, respectively) on bioH(2) production were evaluated in a batch reactor at 35 degrees C, pH 5.5. Microbial community shifts were also analyzed via Illumina MiSeq sequencing. The results showed that the maximum bioH(2) production rate of 107 NmL H-2/Lr h and bioH(2) yield of 115 NmL H-2/g TVSadded were achieved at a vinasse/Nejayote ratio of 80/20. Vinasse and Nejayote were complementary in the concentrations of nitrogen, iron, magnesium, phosphorus and alkalinity. Acetobacter orientalis predominated in the inoculum (42.94%). However, at the exponential phase it was replaced by Lactobacillus casei, Clostridium beijerinckii, Acetobacter lovaniensis and Sporolactobacillus terrae with abundances of 22.03%, 20.27%, 13.39% and 12.96%, respectively. A syntrophy between lactic and acetic acid bacteria, and bioH(2) producers was established. Metabolic profiles showed that bioH(2) and butyrate were produced from acetate and lactate. The microbial structure of the inoculum allowed adaptability to feed the substrates, indicating a high robustness. Thus, it could be employed for bioH(2) production from some other complex substrates. In conclusion, co-digestion of vinasse and Nejayote enhanced the overall bioH(2) production because of their mutual complementarity. (C) 2016 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.