Molecular analyses and biogeochemical measurements were combined to investigate the microbial communities associated with major terminal electron accepting processes and acetate oxidation at 2 contrasting sediments on the continental shelf (EB1) and basin (EB6) of the Ulleung Basin, East Sea. At EB1, sulfate reduction (SR) and iron reduction (FeR) dominated organic carbon (Corg) oxidation, accounting for 65 and 25% of anaerobic Corg oxidation, respectively. In contrast, manganese reduction (MnR) was responsible for >50% of anaerobic Corg mineralization at manganese oxide-rich EB6. Members of Desulfobacteraceae, known as putative sulfate-reducing bacteria (SRB), constituted a major Corg-oxidizing clade (22% of Bacteria) at EB1. Meanwhile, putatively Mn-reducing bacteria affiliated with Colwelliaceae, Shewanellaceae and Oceanospirillaceae were abundant in EB6 (8% of Bacteria). RNA-stable isotope probing (RNASIP) further identified Arcobacter as acetate-oxidizers associated with FeR, while no SRB were labeled at EB1. At EB6, microorganisms affiliated with Colwelliaceae and Oceanospirillaceae were identified as putative Mn-reducing acetate-oxidizers. Interestingly, at both sites, Thaumarchaeota were labeled with 13C derived from acetate during the anoxic incubations. The results from RNA-SIP give new insights into the biogeochemical and ecological role of Arcobacter in FeR, and the metabolic activity of Thaumarchaeota under anoxia. As the upwelling intensity in the UB declines due to the rapid warming of surface waters, our results are relevant for evaluation of future changes in benthic biogeochemical processes and microbial communities in response to the variations of water-column productivity.