Abstract:[Background] Benthic animals are an indispensable constituent of lake eco-environment and play an important role in transformation of nitrogen between sediment and water. There have been showed that benthic animals are the potential source of N2O emission, while the release capability is closely related to habitat environment. The water quality without cyanobacterial accumulation is different from that with cyanobacterial accumulation, which is usually a hot spot of N2O emission. [Objective] To compare the N2O emission of the fresh invertebrates between with and without cyanobacterial accumulation. [Methods] Combing gas chromatography with modern molecular biology techniques, the N2O emission flux and intestinal microbial from Corbicula fluminea were analyzed to extend our knowledge about the microbiology mechanism of N2O emission through laboratory microcosm experiment. [Results] with cyanobacterial accumulation the N2O emission flux of C. fluminea was 447.2 pmol/(ind·h), decreased by about 63% in comparison with control group. The intestinal bacterial and denitrifying bacteria of C. fluminea have different responses to cyanobacterial accumulation. The 454 pyrosequencing revealed that Proteobacteria (β- and δ-), Chloroflexi and Bacteroid were dominant bacteria in control group and occupied about 67.3% of the total bacteria number. While in cyanobacterial accumulation treatment the intestinal microorganism was mainly Proteobacteria (α- and β-), and the relative abundance reached 85.8%. The index of Chao1 and Shannon indicated that the richness and diversity of intestinal bacterial community structure in cyanobacterial accumulation treatment were lower than the intestinal bacterial in control group. Further analysis was conducted on denitrifying bacteria in the intestine of C. fluminea, the result showed that the relative abundance of denitrifying bacteria in cyanobacterial accumulation treatment occupied to 22.6%, which was 2.3 times as much as the control group, thus strengthening the intestinal denitrification. [Conclusion] cyanobacterial accumulation decreased the richness and diversity of the intestine bacteria from C. fluminea, while increased the abundance of intestinal denitrifying bacteria, probably enhanced the complete denitrification, resulting in decreasing the emissions of N2O from C. fluminea. The data obtained in this study could serve as a valuable resource for the environmental effects of benthic animals, which has a great theoretical and practical significance in greenhouse-gas control.