Abstract: High density and intensive Litopenaeus vannamei aquaculture has increased the frequency of shrimp disease, however, it remains uncertain whether change in intestinal bacteria could be indicative of shrimp health state (healthy or diseased). Therefore, we collected water and shrimp intestine samples from ponds with or without diseased shrimps. Using bacterial 16S rRNA gene as a biomarker, the bacterial community structure and diversity were evaluated with the Illumina MiSeq sequencing technique. The results showed that the variations of bacterioplankton community were primarily shaped by the levels of NO₂^--N, chlorophyll a and PO₄^3--P. Bacterial diversity was significantly lower in diseased shrimps than in healthy ones. Using a response ratio analysis, we screened 28 operational taxonomic units (OTUs), and their abundances significantly changed in the intestines between healthy and diseased shrimps. In general, the abundances of OTUs belonged to Actinobacteria, Flavobacteria and Bacilli significantly decreased in diseased shrimps compared with those in healthy shrimps, while the OTUs affiliated to Clostridia showed an opposite pattern. In addition, we obtained 61 indicator species that primarily affiliated to Bacteroidetes, Proteobacteria, Firmicutes, Planctomycetes and Actinobacteria. Notably, the identified indicator taxa exhibited clearly discriminative patterns among habitats (water or intestine) and health status. Collectively, this study provided scientific information for development of new probiotics and disease prevention.