Abstract: To compare the difference of bacterial distribution in water of new or traditional grouper seedling model, the 16S rDNA V4 region of six water samples(A1, A2, B1, B2, C1 and C2)collected from one farm using "the new breeding model of ecological optimization and disease control and prevention" and another traditional model farm on Zhao'an county of Zhangzhou City were sequenced by high-throughput pyrosequencing.Using Qiime and Mothur software, the number of sequences and operational taxonomic units(OTUs)for each sample were sorted and calculated, the species abundance and distribution, Alpha diversity index and difference times of species abundance among samples were analyzed.The number of sequences and OTUs for each sample were 66 727/3 724(A1), 66 418/3 391(A2), 87 403/3 980(B1), 57 519/3 438(B2), 62 349/3 530(C1)and 66 673/3 004(C2).The rarefaction curves showed that adequate sampling was achieved.The number of OTUs was close to actual situation.The value of richness index was 6 535.21/8 872.16(A1), 6 583.85/8 855.40(A2), 8 062.60/10 640.49(B1), 6 878.85/9 352.25(B2), 6 859.85/9 295.45(C1)and 5 291.87/6 868.28(C2); diversity index was 0.05/4.72(A1), 0.04/4.77(A2), 0.04/4.69(B1), 0.04/4.74(B2), 0.05/4.45(C1)and 0.08/4.06(C2).At the time NNV breaking in the traditional model farm, the single sample species abundance, multi-samples species abundance and different times of species abundance at phylum and genus levels between two model samples were analyzed.At phylum level, the distribution of dominant bacterial communities in seedling water between two models were similar.At genus level, the content of pathogenic Pseudomonas of dominant bacterial community in traditional model sample was significantly higher than the new model.Evenness and richness of bacteria flora in the six water samples collected from new and traditional grouper seedling model were obtained before and after the onset of NNV breaking.It was suggested that "the new breeding model of ecological optimization and disease control and prevention" for grouper seedling might good for inhibition of pathogenic bacteria and enrichment of probiotics.