Rice-crayfish integrated system (RC) is a high-efficiency ecological agricultural system which combines the rice planting and crayfish culturing.In order to explore the impact of RC on the microbiome of paddy water,the water microbial diversity and community structure of RC and rice monoculture system (RM) were determined by using 16S rDNA amplicon high-throughput sequencing.The results showed that RC significantly improved the microbial diversity.The microbial community structure of paddy water was significantly different between RC and RM,which could be attributed to water physi-chemical factors,such as total nitrogen and nitrite nitrogen.The relative abundance of Actinobacteria and Cyanobacteria in RC was significantly higher than that in RM,while the relative abundance of Proteobacteria and Bacteroidetes in RC was lower than that in RM.Actinomycetales,Rhizobiales,and Synechococcales are the main biomarkers of water microbiome in RC,while Flavobacteriales,Betaproteobacteriales,and Rhodocyclales are the main biomarkers in RM.Six keystone taxa were identified from the water microbiome in the paddy fields,which mainly belong to Burkholderiaceae,Saprospiraceae and Polyangiaceae.Furthermore,through functional prediction and relative abundance comparison,we found that the metabolic capacity of water microbiome in RC was significantly higher than that in RM,especially the relative abundance of energy metabolism pathway was significantly higher than that in RM.In conclusion,RC formed a better water microbiome with high diversity,stable structure,and strong function and improved the material circulation and energy utilization rate of paddy ecosystem.Those results provide a basis for the utilization of microbial resource in rice-crayfish integrated system.