The Japanese oyster Magallana gigas is one of the most important oysters in aquaculture worldwide. Its production by aquaculture depends on the success of the seed-producing laboratories, which has been variable and attributed to: (1) differences in the quality of the gametes produced by the breeders and (2) poor knowledge of the factors that control their reproductive performance and impact on the offspring. Scientific evidence suggests Highly Diluted Bioactive Compounds (HDBC) as an eco-friendly alternative to improve reproductive performance, immune response, and larval quality in marine species, including oyster mollusks. On the other hand, phytotherapeutic agents such as Phloroglucinol (PHL) , an compound derived from brown algae have functioned as immune response modulators and overexpression of heat shock proteins (HSP) with transgenerational epigenetic effects in Ostrea edulis and Artemia franciscana. Therefore, it is assumed that the application of HDBC and PHL would allow for an increase in reproductive performance, immune response, and larval quality of the Japanese oyster M. gigas , with such an effect on intergenerational inheritance, that it contributes to stabilizing production from seed. To evaluate this hypothesis, an intergenerational experiment will be carried out applying three treatments in organisms of the F0 generation. The experimental design includes a phytotherapeutic (T1; Phloroglucinol), an HDBC formulation (T2; PhA+SiT ), their combination (T3; PhA+SiT + FL), and a control treatment (T4; sea water). The response variables will be zootechnical indicators for the F1 generation and physiological, histological, genetic, biochemical, and epigenetic for the F0 and F1 generation. It is expected that epigenetic modulation strategies with HDBC and PHL will enhance the production of phenotypes with greater productive efficiency and reproductive potential in M. gigas , and that they can be complementary to those currently applied for its traditional genetic improvement. This will allow the generalization of new scientific knowledge on the individual effects of HDBC and PHL, as well as their possible synergistic action as natural and eco-friendly treatments that induce epigenetic changes aimed at the production of phenotypes with greater productive efficiency with potential intergenerational inheritance.