Abstract: In order to elucidate the relationship between "Cryptocaryoniasis" caused by Cryptocaryon irritans infection and secondary bacterial infections in Trachinotus ovatus, in the report, the continuous sampling of the naturally infected fish in offshore deep-sea cage farming systems and the laboratory-reared individuals were conducted, the artificial infection experiments with Cryptocaryon irritans were in order to elucidate the relationship between "Cryptocaryoniasis" caused by Cryptocaryon irritans infection and secondary bacterial infections in Trachinotus ovatus, in the report, the continuous sampling of the naturally infected fish in offshore deep-sea cage farming systems and the laboratory-reared individuals were conducted, the artificial infection experiments with Cryptocaryon irritans were performed, and the correlations between the infection intensity of the parasite, secondary bacterial infection rates, and the hepatic bacterial loads were investigated, and the dominant bacteria in the livers of diseased fish was identified. The results demonstrated that the secondary bacterial infection rates and the hepatic bacterial loads significantly increased with the increase of the severity of Cryptocaryon irritans infection; the peak values of the secondary bacterial infection rates and the hepatic bacterial loads were observed at 168 h post-infection; among 93 dominant bacterial strains isolated from the liver tissues of the farmed Trachinotus ovatus in the natural marine environment, Photobacterium damselae and Vibrio harveyi were identified as the predominant pathogens. This study provides a theoretical basis for the prevention and treatment of Cryptocaryon irritans infection and its associated secondary bacterial infections.