On the basis of a long-term(30 years) field experiment that involved four rotation systems, rice-rice-winter fallow(RRF), rice-rice-ryegrass(RRG), rice-rice-rape(RRP), and rice-rice-milk vetch(RRV), this study described the effects of green manure on the microbial communities in the red paddy soils using 454 pyrosequencing for the 16 S r RNA gene. The Chao1 richness and non-parametric Shannon’s index increased in all soil samples that received green manure treatments. The communities’ structures with the green manure applications were significantly dissimilar from that under the winter fallow. Using Metastats tests, many genera in the RRG, RRP and RRV soils were significantly different from those in the RRF soil, including a number of genera that functioned in the nitrogen and sulfur cycles. Analyses of the genera with these functions revealed the shifts in microbial ecosystem functions after long-term green manuring. Changes in the microbial communities increased the ammonium supply and decreased the soil acidification in green-manure-amended soils. Together, these data suggested powerful effects of green manure on both the microbial communities and the biogeochemical cycle driven by the shifts in bacterial functional groups. On the basis of a long-term (30 years) field experiment that involved four rotation systems, rice-rice-winter fallow (RRF), rice-rice-ryegrass (RRG) -rice-milk vetch (RRV), this study described the effects of green manure on the microbial communities in the red paddy soils using 454 pyrosequencing for the 16S rRNA gene. The Chao1 richness and non-parametric Shannon’s index increased in all soil Samples that received green manure treatments. The communities’ structures with the green manure applications were significantly dissimilar from that under the winter fallow. Using Metastats tests, many genera in the RRG, RRP and RRV soils were significantly different from those in the RRF soil, including a number of genera that functioned in the nitrogen and sulfur cycles. Analyses of the genera with these functions revealed the shifts in microbial ecosystem functions after long-term green manuring. Changes in the microbial communities increased the ammonium supply a nd decreased the soil acidification in green-manure-amended soils. Together, these data said powerful effects of green manure on both both microbial communities and the biogeochemical cycle driven by the shifts in bacterial functional groups.