Paddy soil bacterial community structure was studied through 16S rDNA gene. The soil samples were collected from the long-term fertilization experiment field at the Taoyuan Agro-ecosystem Research Station. Total microbial DNA was directly extracted from both treatments including amended with rice straw (OM) and CK. The clone libraries were constructed after cloning and sequencing. The result showed that the bacterial communtiy composition of the paddy soil amended with rice straw (OM) was changed significantly compared with CK, both Shannon index and evenness decreased indicating its bacterial diversity was decreased. Proteobacteria were predominated both in rice straw (OM) and CK treatments, followed by Acidobacteria. Application of rice straw induced obvious decrease of the genotypes of Proteobacteria, Verrucomicrobia, Chloroflexi and Chlorobi compared to CK, in the contrast, the genotypes of Nitrospira increased. The phylogenetic tree based on the 16S rDNA sequences showed that application of rice straw varied the distribution of Acidobacteria greatest, followed by Verrucomicrobia and Delta-Proteobacteria. Therefore, application of rice straw had an important impact on bacterial community structure.