Abstract Highly diluted bioactive compounds (HDBC) and highly diluted immunomodulatory compounds (HDIC) are treatments that cover a wide variety of concentrations, starting from molar to yoctomolar concentrations or even lower where the presence of nanoparticles has been detected. The prophylactic use of these compounds has improved nutrition, growth, overall condition, defence mechanisms regulation and increased marine organism survival during challenge against pathogens. The HDBC used in marine organisms are formulated from Vibrio spp. lysates, sodium metasilicates, phosphoric acid and highly diluted drugs for humans as Silicea terra ® , Phosphoricum acidum ® , Passival ® and VidatoX ® , as well as homotoxic Heel ® complexes. Because HDBC are innocuous, inexpensive and easy to use by immersion or ingestion, they have been proposed as a potential sustainable alternative to improve marine organism production under hatchery conditions and reduce the use of chemotherapy, including antibiotics and disinfectants. Nonetheless, articles documenting their mode of action (biological process and metabolic pathways activated) are scarce. Some studies have proposed that certain HDBC activate the sentinel system of marine organisms, such as non‐self‐recognition and endocytosis mechanisms without completely activating the immune defence mechanisms. This contribution brings a new insight on increasing productivity and cost effectiveness during hatchery operations and at the same time strengthening the immune system response and survival of marine organisms against infections. Therefore, this review discusses and analyses published results of HDBC in species of commercial importance worldwide and also emerging species of interest for aquaculture reared in Mexico.