Marine microalgae are potential producers of antimicrobial compounds. Monospecific, vibrio-free co-cultures of marine microalgae, Chaetoceros calcitrans, Tetraselmis suecica, Nannochloropsis sp. and Thalassiosira weissflogii, at the exponential phase of growth were inoculated with two Vibrio parahaemolyticus (Vp) strains. Vp M0904, a highly virulent strain responsible for acute hepatopancreatic necrosis disease (AHPND), and Vp M0702, a non-pathogenic strain, both at 1 × 105 CFU ml−1. Microalgae and bacterial growth, total lipids and carbohydrates were obtained at 1, 2 and 3 days post inoculation with bacteria. Ethanolic (EE) and seawater extracts (SE) of C. calcitrans were also obtained to evaluate the inhibitory activity against Vp M0904. Microalgae cellular growth was not affected by any tested bacteria throughout the experiment; in contrast, Vp M0904 was significantly (p < 0.05) inhibited in co-culture with C. calcitrans and T. suecica. Meanwhile, Vp M0702 was significantly (p < 0.05) inhibited by all microalgae except for Nannochloropsis sp. Minor, non-significant variations were found in the lipids and carbohydrate metabolism of all microalgae inoculated with both strains. Low CFU ml−1 of Vp M0904 was registered when it was incubated with SE of C. calcitrans at concentrations over 75 µg ml−1, however, EE did not show any antibacterial activity. The bacteriostatic effect was dependent of microalgae type and Vibrio strain. Hydrophilic compounds of C. calcitrans cells possess antibiotic activities on the highly virulent Vp M0904 responsible for AHPND, a devastating disease for farmed shrimp around the world.