Abstract: Paddy soils not only function as an important sink for “missing carbon” but also play an important role in the production of greenhouse gases such as N₂O and CH₄. Dynamic changes in greenhouse gases in the atmosphere are closely related to microbially mediated carbon and nitrogen transformation processes occurring in soil. Using soil samples collected from a longterm fertilization experimental site in Taojiang County, subtropical China (established in 1986), we determined the effects of longterm (>25 years) nonfertilization (CK), chemical fertilization (NPK), and NPK combined with rice straw residues (NPKS) on soil bacterial  and archaeal community structures. The 16S rRNA genotypes from the three differently treated soils were divided into 9 bacterial phylotypes, mainly including Proteobacteria, Acidobacteria, Chloroflexi, and archaea of Crenarchaeota and Euryarchaeota. The relative abundance of Proteobacteria, Acidobacteria and Crenarchaeota increased in the soils under NPK and NPKS treatments, with the increase being greater in the latter treatment. LUBSHUFF statistical analyses also demonstrated that there was significant difference among the microbial community compositions in CK, NPK and NPKStreated soils. The abundance of bacterial and archaeal 16S rRNA genes ranged from 0.58 × 10¹⁰ to 1.06 × 10¹⁰ copies·g^-1 dry soil and from 1.16 × 10⁶ to 1.72 × 10⁶ copies·g^-1 dry soil, respectively. Application of fertilizers increased the bacterial and archaeal abundance and diversity in the treated soils, with NPKS>NPK. Longterm chemical and organic applications significantly affected the abundance, diversity and composition of bacterial and archaeal communities in paddy ecosystems.