Effects of transgenic rice on the structure and function of soil microbial community were studied by the methods of DGGE and Biolog. Two varieties of transgenic rice were tested and compared with their controls, the nontransgenic isolines. The results showed that the transgenic rice had a significant effect on the number of bacteria, only in fastgrowing period. The genetic distance between two varieties of transgenic rice was greater than the distance between the transgenic rice and its nontransgenic parental rice, which implied there was little effect on the genetic diversity of soil microbial communities. In the whole growing period of rice, the amount of average well color development (AWCD) were observed in the soil microbial communities of two varieties of transgenic rice after 72 h, as compared with the control. A significant difference appeared at heading stages, while disappeared at maturity stage. The diversity index and evenness index of soil microbial communities had the similar trend. The results proved that Mclntosh index (u) could effectively distinguish transgenic rice and its nontransgenic parental in vigorously growing stage.