In countries where concentrated animal feeding operations (CAFOs) are used, implementation of animal waste treatment is desired for both environmental protection and energy recovery. In the US, 1.4 billion tons of animal waste is generated annually. The capability of anaerobic systems to produce large quantities of biogas from animal wastes has been demonstrated, however, a lack of knowledge on the microbial community structure exists. Four 5-liter anaerobic sequencing batch reactors (ASBRs) were operated over a period of 988 days to treat swine waste (with a volatile solids concentration of 20 g VS/L). During the first operating period (0-378 days), all four ASBRs were maintained at similar conditions. The total ammonium concentration was maintained at 1,200 mg NH₄⁺-N/L at a temperature of 25°C, while solids loading rates were gradually increased from 1 to 4 g VS/L/day. During the second operating period (379-745), the total ammonium concentration for two of the four reactors was increased to 4,400 mg NH ₄⁺-N/L. Next, the temperature was raised from 25°C to 35°C in all reactors during the third period (746-988). The total ammonium levels were initially maintained according to period 2, and gradually were then increased up to 5,200 mg NH₄⁺-N/L. The performance of the bioreactors was assessed with conventional environmental engineering techniques, and archaeal and bacterial microbial communities were unraveled with molecular biology techniques. The methane yield was not statistically different among the four reactors in period 1 (0.31 L CH₄/g VS). In period 2, the methane yield was 45% lower for the high-ammonia reactors compared to low-ammonia reactors. This methane production inhibition by ammonia was alleviated to 13% in period 3 with a higher operating temperature of 35°C, showing that microbial metabolism rates (i.e., kinetics) overcame toxicity constraints. The bacterial community analyses did not show a significant difference between low- and high-ammonia reactors for different temperatures at the phyla level, with Firmicutes (∼46% of the bacterial community; the bacterial population computed ∼65% of the total microbial community structure) and Bacteroidetes (∼33%) as the predominant phyla. Members of the family Methanosarcinaceae (from 3% to 8% of the total microbial community) and of the order Methanomicrobiales (also between 3% and 8%) predominated as acetoclastic and hydrogenotrophic methanogens, respectively. The performance of the anaerobic digesters was clearly affected by varying total ammonium concentrations and mesophilic temperatures, however this did not result in a microbial community shift. Carbon and energy sources outplayed toxicity effects of ammonia and temperature constraints of kinetics and thermodynamics in determining the microbial community in our bioreactors.