Abstract: The composition, diversity, microbial predicted functions and interspecific interactions of the intestinal and hepatopancreatic flora between healthy shrimp and diseased shrimp infected with Hepatocystis hepatica were investigated comparatively using 16S rRNA high-throughput sequencing. The results showed that the diversity of bacterial communities in the intestinal and hepatopancreas was higher in healthy shrimp compared to affected shrimp. At the genus level, the composition and abundance of the dominant bacteria differed significantly in the intestine and hepatopancreas of healthy and diseased shrimp. In the intestine of healthy shrimp, Escherichia-Shigella and Spongiimonas were the dominant genera, while Shewanella, Megasphaera, Klebsiella, Pseudomonas and Halomonas were the dominant genera in the intestine of diseased shrimp. In the hepatopancreas of diseased shrimp Cupriavidus were the dominant genus. Tax4Fun2 predicted that the main functions of the intestinal and hepatopancreatic flora of healthy shrimp differed significantly from those of diseased shrimp. This study provides valuable insights into the effects of hepatic intestinal cysts on bacterial communities in the intestine and hepatopancreas of Litopenaeus vannameis, facilitating healthy management and culture of this shrimp species.