Leakage of O2 from roots of aquatic plants supports the oxidation of ammonia to nitrate and of sulfide to sulfate in the rhizosphere, so that these electron acceptors may become available to the root microbial communities and affect their activity. We studied the composition of the bacterial community active in anoxically incubated rice roots by analysis of terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequencing targeting bacterial 16S rRNA. The bacterial ribosomal abundance in unamended rice roots, which were naturally encrusted with ferric iron, were initially dominated (about 65% of total 16S rRNA) by Clostridium, Bacillus and Geobacter/Pelobacter, but after 5 d clostridia decreased and members of the Cytophaga–Flavobacterium–Bacteroides (CFB) phylum increased (up to 30% of total 16S rRNA). Addition of nitrate or sulfate to the root incubations resulted in bacterial growth detected by fluorescent in situ hybridization (FISH). It also affected the steady state concentrations of H2, acetate, propionate and butyrate that were measured in the root incubations. Nitrate reducers were apparently involved in consumption of all of these compounds. Sulfate reducers, on the other hand, showed net production of acetate during utilization of propionate. Nitrate stimulated populations of Bacillus and Dechloromonas to become active, the latter temporarily increasing to 25% of total 16S rRNA, but suppressed the increase of CFB bacteria. Sulfate, on the other hand, stimulated Desulfosporosinus and Geobacter/Pelobacter, increasing to about 15% of total 16S rRNA, and suppressed CFB bacteria to become active. In conclusion, our study showed the potential effect of exogenous electron acceptors on the composition and activity of the bacterial community in rice root incubations, and identified the phylogenetic groups of the root microbial communities that respond to an increased availability of nitrate or sulfate.