Anaerobic digestion (AD) of Ulva biomass, a promising next-generation feedstock for energy production, was investigated in sequencing batch mode. Over five cycles of operation, the methane yield decreased more than twofold (from 0.15 to 0.07 L/g CODfed), while the organic treatment efficiency (i.e., chemical oxygen demand (COD) removal) remained fairly constant (53.7-61.1%). Such changes in reactor performance were related with structural variations in the microbial community, particularly the bacterial community, with repeated cycles. Methanosaeta- and Methanolinea-related populations were most likely the main aceticlastic and hydrogenotrophic methanogens, respectively, in the reactor. The emergence and prevalence of sulfate-reducing bacteria (SRBs), primarily a Solitalea-related population, most likely resulted in increased consumption of organic substrates for sulfate reduction, rather than methane production, in later cycles. Our observations suggest that the metabolic properties of the reactor changed with the transition of the bacterial community structure over cycles, and the metabolic shift had a negative effect on methanogenesis. The sequencing batch operation strategy applied in this study was not suitable for maximizing methane production from Ulva biomass, although the treatment efficiency was fairly stable. Robust control of SRB activity is necessary for more stable and efficient biomethanation of Ulva biomass in sequencing batch mode. (C) 2016 Elsevier Ltd. All rights reserved.