The biogenic hydrogen production by dark fermentative digestion of biomass shows excellent potential for solving the recent energy difficulties. To augment the efficiency of this process, the biochemical degradation needs to be understood better. The physical optimum (PhO) method was found to be particularly suitable to illustrate the maximum potential of the process. It is based on a theoretical, ideal reference state. For this purpose, the dark fermentation was modeled mathematically using Petri nets, a modeling language based on graph theory. The Petri net model was developed based on the biochemical reactions system of anaerobic digestion. All degradative steps relevant to hydrogen production were included. Then the modeled metabolic rates were analyzed to be used as a reference base in evaluating the process’s efficiency. This ideal reference state, the anaerobic digestion’s PhO, was compared with experimental data by the PhO factor. This factor summarizes the efficiency of the whole process.