Aims Microbial community associated with hydrogen production and volatile fatty acids (VFAs) accumulation was characterized in acidogenic hydrogenesis using molasses wastewater as a feedstock. Methods and Results Hydrogen and VFAs production were measured under an organic loading rate (OLR) from 19 to 35 g‐COD l−1 day−1. The active microbial community was analysed using RNA‐based massively parallel sequencing technique, and their correlation patterns were analysed using networking analysis. The continuous stirred tank reactor achieved stable hydrogen production at different OLR conditions, and the maximum hydrogen production rate (HPR) was 1·02 L‐H2 l−1 day−1 at 31·0 g‐COD l−1 day−1. Butyrate (50%) and acetate (38%) positively increased with increase in OLR. Total VFA production stayed around 7135 mg l−1 during the operation period. Although Clostridiales and Lactobacillales were relatively abundant, the HPR was positively associated with Pseudomonadaceae and Micrococcineae. Total VFA and acetate, butyrate and propionate concentrations were positively correlated with lactic acid bacteria (LAB) such as Bacillales, Sporolactobacillus and Lactobacillus. Conclusions The close relationship between Pseudomonadaceae and Micrococcineae, and LAB play important roles for stable hydrogen and VFA production from molasses wastewater. Significance and Impact of the Study Microbial information on hydrogen and VFA production can be useful to design and operate for acidogenic hydrogenesis using high strength molasses wastewater.