Abstract: In this exp eriment, the pathogenic fungi of fresh garlic were isolated, identified and controlled during late storage period. Three fungal strains were isolated from the diseased fresh garlic, and back inoculated to healthy fresh garlic. Then the corresponding pathogenic fungi were re-isolated from the diseased fresh garlic, and the antibacterial experiments of ozone with different concentrations and treatment time on these purified strains were determined. Results showed that these extracted strains were isolated and identified as Alternaria, Penicillium chrysogenum, and Paecilomyces cateniobliquus Liang, respectively. Alternaria was determined as the main pathogenic fungus depending on the morbidity, which was consistent with natural onset symptoms. Antibacterial test results showed that ozone treatment with 21.44 mg/m~3 for 12 h at 0 ℃ presented superior inhibitory effects on the incidence of Alternaria infection in garlic.