Simple Summary The maintenance of animal health and preventing disease is an important point for sustainable aquaculture. In this sense, medicinal herbs can help farmers to achieve this goal. Although many review articles have discussed the effects of these additives on growth performance, immune and antioxidant responses, as well as resistance to diseases in fish, limited knowledge is available on how herbs affect these parameters at the molecular level. Given that studies at the molecular level can provide an accurate picture of the mode of action of feed additives, in this paper, the results of studies focusing on the effect of herbs on the expression of different genes in fish are discussed. The crucial need for safe and healthy aquatic animals obligates researchers in aquaculture to investigate alternative and beneficial additives. Medicinal herbals and their extracts are compromised with diverse effects on the performances of aquatic animals. These compounds can affect growth performance and stimulate the immune system when used in fish diet. In addition, the use of medicinal herbs and their extracts can reduce oxidative stress induced by several stressors during fish culture. Correspondingly, aquatic animals could gain increased resistance against infectious pathogens and environmental stressors. Nevertheless, the exact mode of action where these additives can affect aquatic animals' performances is still not well documented. Understanding the mechanistic role of herbal supplements and their derivatives is a vital tool to develop further the strategies and application of these additives for feasible and sustainable aquaculture. Gene-related studies have clarified the detailed information on the herbal supplements' mode of action when administered orally in aquafeed. Several review articles have presented the potential roles of medicinal herbs on the performances of aquatic animals. However, this review article discusses the outputs of studies conducted on aquatic animals fed dietary, medicinal herbs, focusing on the gene expression related to growth and immune performances. Furthermore, a particular focus is directed to the expected influence of herbal supplements on the reproduction of aquatic animals.