A large number of Carassius auratus gibelio and Hypophthalmichthys molitrix young fishes died in the polyculture ponds. In order to ascertain the etiology, tissue injury and provide disease prevention and control measures, macroscopic and microscopic examinations, bacteriological detecting, virological detecting, histopathological observation and drug susceptibility test were operated on the diseased fish. The results showed that there were a few Apiosoma sp. and Trichodina sp. on the body surfaces of diseased fish, which would not cause death and the symptoms of hyperemia and hemorrhage. No other parasitical and fungal pathogens were found. Isolated strains from diseased fish were identified as A. hydrophila by their morphological observation, physiological and biochemical characteristics, and sequence analysis of the 16S rRNA gene. According to the present situations of C. auratus gibelio and H. molitrix viral diseases, one pair of specific primer for PCR amplification of Cyprinid herpesvirus 2(CyHV-2) DNA polymerase gene was used to detect CyHV-2 in diseased fish. CyHV-2 was detected only in diseased C. auratus gibelio. The aseptic supernatants of homogenated tissues from naturally diseased C. auratus gibelio and H. molitrix were respectively used for the artificial infections. Only the former caused healthy C. auratus gibelio to display the clinical sign of hyperemia and to die. It was concluded from the results that A. hydrophila was the main pathogen of diseased C. auratus gibelio and H. molitrix and CyHV-2 was the secondary pathogen of the diseased C. auratus gibelio. There were similar histopathological changes in both of the diseased H. molitrix infected only with A. hydrophila and diseased C. auratus gibelio infected with mixed infections of A. hydrophila and CyHV-2. There were specific histopathological changes in each kind of diseased fish. Granular degeneration of liver and kidney appeared in the mild pathologic lesions and the nuclei of necrotic cells were mainly karyolysis in diseased H. molitrix. Hyaline degeneration of liver appeared in the mild pathologic lesions, the nuclei of necrotic cells were mainly karyopyknosis and karyorrhexis and the hypertrophied cell nuclei with marginated chromatin appeared in the kidney and spleen in diseased C. auratus gibelio. The main organs lost their functions as the result of undergoing the pathological processes from degeneration to necrosis and both kinds of diseased fish died eventually. The results of antimicrobial susceptibility tests suggested that Norfloxacin and Florfenicol could be used to prevent and control A. hydrophila infection. CyHV-2 vaccine and ecological farming methods could be used to prevent and reduce the viral infection and viral development in diseased C. auratus gibelio.