This study aims to screen and evaluate the antibacterial activity of methanolic extract from marine fungi against pathogenic vibrios. The resazurin-based assay was optimized for high-throughput screening of anti-Vibrio agents. Determination of minimum inhibitory concentrations of the test antibiotics ciprofloxacin and erythromycin against three pathogenic Vibrio strains revealed that the optimized assay can accurately measure antibacterial activity. A total of 1516 methanolic fractions of ethyl acetate extracts from 32 marine fungi were screened by the optimized assay, and four fractions were identified to have significantly inhibitory effect on all three test Vibrio strains. Among these, fraction Z16-17 derived from Schizophyllum commune MCCCZ16 showing strong anti-Vibrio activities and nontoxicity was evaluated for efficacy against experimental Vibrio vulnificus infection in white shrimp (Litopenaeus vannamei). Shrimp fed with fraction Z16-17 supplemented diet at 50, 100 and 200 μg/g for seven days showed notably higher survival rate than the control group fed with unsupplemented diet. Results suggested that the resazurin-based assay can be a reliable method to screen large chemical or natural product libraries for anti-Vibrio activity, and fraction Z16-17 has a good potential to reduce the negative impact of pathogenic vibrios in shrimp aquaculture.