The disease outbreak of Chinese perch poses a severe threat to aquaculture industry. To explore the relationship between microbial communities in farming water and those in the intestine, and to further reveal the relationship between fish disease and environmental microbes (internal and external environments), 16S rRNA were sequenced. Although the composition and abundance of bacterial phyla varied with month in water samples, Actinobacteria and Proteobacteria were always the top 2 dominant phyla. Furthermore, most dominant genera in water were not significantly affected by environmental factors and seasonal changes, but there were specific dominant genera for each month. Besides, most dominant genera in water were not pathogenic bacteria. The Chinese perch ponds often breakout disease in September. 16S rRNA of the gut samples from the diseased and healthy Chinese perch were sequenced. In September, high water temperature and high contents of nitrite and ammonia-N might be environmental factors causing the disease outbreak of Chinese perch. The gut samples presented similarity in the phylum categories between the diseased and healthy Chinese perch, but they exhibited different abundances of microbiota at phylum level. Fusobacteria (44 %) exhibited the highest abundance in diseased Chinese perch, whereas Firmicutes (58 %) displayed the highest abundance in healthy Chinese perch. In addition, Lactococcus were dominant genus in September water samples and gut samples from diseased fish, which might be the pathogenic bacteria to infect the Chinese perch. Our findings provide novel information for improving microbial communities in aquaculture environments.