Increasing pace in aquaculture development to meet the growing food requirements of the population has greatly compromised the carrying capacity of the culture environment and has placed the aquacultured animals at heightened risk of getting diseases due to pathogens. At present, chemotherapy is widely used as means to prevent or treat infectious diseases in aquaculture; however, the use of these drugs poses multiple negative impacts on fish and human health, as well as the environment. Recently, research initiatives are focused on the use of plant products and their derivatives as a means of controlling diseases in aquaculture. They are regarded as a promising alternative to the use of chemical treatments for infectious diseases in fish. Plant-derived products or phytogenics have been shown to stimulate appetite and promote weight gain in farmed animals, act as immunostimulants, and possess potent anti-pathogenic properties in fish. Their potency is mediated by the presence of bioactive molecules including alkaloids, terpenoids, saponins, and flavonoids, among others. Moreover, nutritional strategies are geared towards the use of these phytogenics in modulating immune and physiological responses, as well as promoting optimum health and microbial community in the gastrointestinal tract of fish. This review synthesizes the current knowledge on the use of phytogenic feed additives in aquaculture by focusing on how these substances act as modulators of health and bacterial community in the gut of fish.