The fermentative hydrogen production occurs during the anaerobic digestion of organic matter. It is a promising technology to produce renewable energy. However, the mixed culture fermentation performances vary considerably depending on the operating conditions such as pH. We investigated the potential of a molecular CE-SSCP (capillary electrophoresis-single strand conformation polymorphism) fingerprinting method based on the hydA functional genes to better describe the bacterial community dynamics, with regards to the standard 16S rDNA-based method. A series of batch experiments was performed from sucrose at different initial pH from 4 to 6. As expected, the highest H2 production potentials (Hmax) and rates (Rmax) were obtained at the highest pH. Changes in batch performances were clearly associated with shifts in the hydA diversity and structure. In contrast, 16S rDNA-based fingerprints were less sensitive to changes in H2 production performances. The Hmax was related to lower hydA diversity, with Clostridium sporogenes as the major H2 producer. Communities harboring larger hydA diversities were found in experiments with the higher Rmax, suggesting that species coexistence may have positive effects on H2 production.