Using the new high-throughput sequencing technique, study was carried out on responses to elevated CO₂ (e CO₂) of endophytic bacteria at the whole microbial community level in the roots of ZhenXian-96 (ZX-96), YangDao-8 (YD-8), II You-084 (TY-084), and YangLiangYou-6 (YLY-6), commonly used in the FACE experiment in China. Results show that the family of Enterobacteriaceae within the class of γ-proteobacteria was the highest in relative abundance, accounting for 30.8%~59.8% of the whole community. In ZX-96, YD-8, and TY-084，e CO₂ would probably inhibit growth of the microbial groups that are dominant in population (dominant groups) but stimulate growth of those that are less (rare groups). For instance, in rice TY-084, Enterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae, and Aeromonadaceae were the four dominant bacterial groups, of which each exceeded 14.6% in relative abundance, and their total relative abundance declined from 74.8% to 67.2% under e CO₂. On the contrary, the rare groups in the roots, consisting of Sphingobacteriaceae, Comamonadaceae, Flavobacteriaceae, and Oxalobacteraceae, increased from 4.13% to 16.9% in total. Especially the family of Sphingobacteriaceae increased by up to 344 folds, and hence is the microbial group the most sensitive to e CO₂. However, in YLY-6, the responses of endophytic bacteria differed in pattern from those in other varieties of rice. These findings indicate that relative abundance of microbes may probably be an important factor affecting the response of endophytic bacteria in the roots to elevated CO₂, which may be used as certain basis for the study on variation of structure and function of the whole microbial community in response to the global climate change.