Abstract: Gastroenteritis is a common disease in the artificial breeding process of Hippocampus, which is mainly caused by bacterial infection, and is highly contagious and harmful. Therefore, it is of great significance to analyze the composition of bacterial community in the intestines of Hippocampus infected with gastroenteritis for the diagnosis and prevention of gastroenteritis. The intestinal structure of healthy and diseased Hippocampus abdominalis were collected, and the high-throughput sequencing of bacterial 16Sr DNA fragments and bioinformatics analysis were used to explore the structural characteristics of intestinal bacteria in the hippocampus infected with gastroenteritis. The results showed that there were significant differences in the intestinal bacterial diversity and structure between the healthy and diseased Hippocampus. At the genus level, the dominant intestinal bacteria of diseased Hippocampus were Vibrio, Vagococcus, and Mycobacterium, while the dominant intestinal bacteria of healthy Hippocampus were Roseibium, Bacteroidales_unclassified, Vibrio, and Psychrobacter. The common genera of the healthy and diseased Hippocampus included Vibrio, Aliivibrio, Bacteroidetes_unclassified, and Photobacterium. Compared with the intestinal flora of healthy Hippocampus, the content of Vibrio and Aliivibrio in the intestines of diseased Hippocampus was significantly higher than that of healthy Hippocampus. Besides, there were some unique bacterial genera in the intestines of diseased Hippocampus, such as Mycobacterium, Bacteroidales_unclassified, Tenacibaculum, and Shewanella. The results of the study analyzed the possible pathogenic bacteria in the intestines of Hippocampus infected with gastroenteritis, which would be of important guiding significance for the prevention and control of diseases in the breeding process of Hippocampus.