Zooshikella marina, a marine bacterium that produces a red pigment, has been shown to possess various antimicrobial activities. The present study reports on in vitro antibacterial activity of cell and extract from Z. marina against Vibrio parahaemolyticus, V. harveyi, V. alginolyticus and V. vulnificus, responsible for vibriosis in aquatic animals. Cross streak and agar well‐diffusion techniques revealed the inhibitory effects of Z. marina against V. harveyi, V. alginolyticus and V. vulnificus. The minimum inhibitory concentration and minimum bactericidal concentration of Z. marina extract against pathogenic bacteria ranged from 64 to 1,024 µg/mL. A time‐kill kinetics assay showed that treatments with Z. marina extract significantly reduced the numbers of viable V. harveyi, V. alginolyticus and V. vulnificus from those in control groups (p<0.05). Electron microscopy showed morphological changes of pathogenic bacteria exposed to the extract, revealing irregular, ruptured and dead cells when treated with 0.25xMIC. In addition, Vibrio spp. cells pre‐treated with the extract were more sensitive to lysozyme and H2O2 than untreated cells. Determination of cytotoxicity indicated that Z. marina extract at concentrations of 1.95–1,000 µg/mL did not show haemolytic activity towards Asian seabass (Lates calcarifer) erythrocytes. In vivo study on invasion and persistence in Asian seabass fed with dietary supplementation with cell and extract from Z. marina revealed significantly decreased V. vulnificus from the fish tissue within 5–14 days (p<0.05). Our findings reveal the potential antimicrobial activity of Z. marina cell and its extract which is safe and could be used in controlling vibriosis in aquaculture.