Two temperature-phased anaerobic digestion (TPAD) systems, with the thermophilic digesters acidified by acidogenesis products (AT-TPAD) or operated at neutral pH and balanced hydrolysis/acidogenesis and methanogenesis (NT-TPAD), were evaluated to treat high-strength dairy cattle manure. Despite similar methane productions (about 0.22 L/g VS fed), the NT-TPAD system removed significantly more VS (36%) than the AT-TPAD system (31%) and needed no pH adjustments. The thermophilic digester of the NT-TPAD system dominated the system performance and performed significantly better than that of the AT-TPAD system. The opposite held true for the mesophilic digesters. Differences of the thermophilic digesters between two TPAD systems affected the microbial communities of both local and downstream digesters. Each digester harbored distinctive microbial populations, some of which were significantly correlated with system performance. Methanosarcina was the most important methanogenic genus in both TPAD systems, while Methanosaeta only in the NT-TPAD system. Their populations were inversely related to VFA concentrations. (C) 2013 Elsevier Ltd. All rights reserved.