A 6-L, completely mixed anaerobic bioreactor with an external ultrafiltration membrane module was operated for 300 days to evaluate the startup and performance of an anaerobic membrane bioreactor (AnMBR) treating swine manure. The reactor had a successful startup at the initial loading rate of 1 g volatile solids (VS)/L/day. After a two-fold increase in loading rate followed by a sudden, two-fold increase in flow velocity through the membrane module on day 75, the performance of the AnMBR deteriorated as measured by volatile fatty acid (VFA) accumulation, decrease in pH, and decrease in biogas production. The methanogenic population dynamics in the reactor were monitored with terminal restriction fragment length polymorphism (T-RFLP). Changes in the relative levels of Methanosarcinaceae and Methanosaetaceae were consistent with changes in VFA concentrations, i.e., high and low levels of acetate corresponded to a high abundance of Methanosarcinaceae and Methanosaetaceae, respectively. The levels of hydrogenotrophic methanogens of the order of Methanomicrobiales increased during decreased reactor performance suggesting that syntrophic interactions involving hydrogenotrophic methanogens remained intact regardless of the degree of shear in the AnMBR.