This paper explores the possibility of using the supernatant of Haslea ostrearia culture containing marennine, a natural microalgal pigment, as an antimicrobial in bivalve hatcheries. The use of known antibiotics to control diseases is generally avoided in hatcheries, as they are expensive, may leave harmful compounds, and may cause the development of antibiotic-resistant bacterial strains. Hence, there is a need to identify new molecules with antimicrobial activities and marennine could be such a molecule. The blue mussel Mytilus edulis, the scallop Placopecten magellanicus and the oyster, Crassostrea virginica were used as model animals, and the pathogenic marine bacteria Vibrio splendidus was used to induce larval mortality. The hypothesis tested was that V. splendidus pathogenicity in larval rearing can be controlled by using marennine-containing culture supernatants. The effect of three marennine concentrations were tested on a larval rearing over 20 days for mussels and oysters and 9 days for scallops. At a low dose (0.1 mg L−1), survival and physiological condition were both higher than in the control. In bacterial challenges, larvae were exposed to V. splendidus for 72 h, with or without marennine. The bacterial challenge caused significant mortality when compared to controls, while the marennine-treated larvae showed significantly higher survival. With use of nuclear magnetic resonance, we demonstrated than marennine acts on V. splendidus through a stiffening mechanism, which could imply interaction with lipopolysaccharides in the outer membrane and/or stress-induced isomerization of unsaturated fatty acids. Results show that marennine is an interesting molecule for pathogen control in hatcheries as it is active at low concentrations and significantly enhanced larval survival and physiological condition.