The factors of alternating flooding and draining during the vegetative growth phase and applying compost to investigate changes in bacterial community composition between the system of rice intensification (SRI) and conventionally managed rice were investigated. 16S rRNA gene T-RFLP analysis showed the major changes in the bacterial communities from the beginning of cultivation to vegetative phase, at which time the groups formed remained consistent until the end of cropping season. Significant and consistent separations of microbial communities between the two systems were revealed. These results suggested that the differences in rice cultivation practice can cause the changes in microbial communities.