Single-stage and two-stage anaerobic digesters treating synthetic primary sludge were operated for over 300 days and compared with respect to methanogen community structure and digester function. Community structure was characterized using banding pattern intensities from denaturing gradient gel electrophoresis (DGGE) for the mcrA gene of methanogenic Archaea. Function was described using specific methanogenic activity (SMA). All digesters were seeded with the same biomass, but different methanogen communities developed over time in the staged and unstaged digesters. Compared to a single-stage CSTR, staging increased the SMA by 41, 26, and 57% with propionate, acetate, and hydrogen, respectively. Additionally, the staged digester produced 10% more methane and achieved 10% greater volatile solids (VS) destruction. Process configuration shifted the methanogen community structure, and this impacted digester function.