AbstractTilapia (Oreochromis sp.) are the most widespread aquaculture species grown and are expected to continue increasing in production to meet the growing demand for fish by an ever‐increasing human population. Fish health management is one of the major concerns in the production of aquaculture species. A number of studies have been conducted to identify new procedures for reducing disease of commonly farmed species, such as tilapia. To prevent disease, the use of antibiotics is common practice in most aquaculture facilities. However, consumer demand and increasing incidence of antibiotic resistance have caused the reduction in the use of antibiotics being administered regularly. A recent strategy is the incorporation of antibiotic alternatives, such as probiotics, prebiotics, and alternative carbohydrate ingredients to promote the growth and health of the fish through the modulation of gastrointestinal microbiota. Intestinal autochthonous microbiota fulfils a number of important roles in host digestion, immunity and intestinal integrity. In the past, the majority of studies on the intestinal microbiota of tilapia used culture‐based methods that are not representative of the entire community. With the advancement of molecular techniques, current studies are utilizing culture‐independent methods to monitor the microbial modulation in the tilapia gastrointestinal tract. This review discusses the effects of antibiotics, probiotics, prebiotics and alternative feed ingredients on the intestinal microbiota of tilapia using culture‐independent techniques. Although advances have been made in the understanding of tilapia intestinal microbiota, more research is needed into the microbial ecology, alternative feedstuff effects and economic impacts of modulating intestinal microbiota of tilapia.