In this study, 454-pyrosequencing technology was employed to investigate the microbial community structure in grass carp culture water with or without different probiotics. The results showed that all three treatments remarkably increased the bacterial diversity compared to the control. In two samples (Control and CB), the dominant phylum was Proteobacteria. However, there was only moderate difference in the content of Proteobacteria and Actinobacteria between sample BS and PSB. Actinobacteria and Bacteroidetes in PSB, BS, and CB were more abundant than those in the control group. The detailed analysis of Proteobacteria showed that in PSB, BS and CB samples, the majority of Proteobacteria consisted of subdivision, followed by Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria; in the control sample, the dominant subtype was Gammaproteobacteria, followed by Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. For Bacteroidetes, Flavobacteria was the dominant subtype in treated samples but not in the control sample. At the order level we also oberseved a marked difference between the control and the treatment in terms of the composition of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Bacteroidetes. The results indicated that the addition of different probiotics into water could increase the diversity and alter the structure of a microbial community.