With the rapid growth of global tilapia aquaculture, improving tilapia health and production through better farm management is critical. Studies have recognized the significant role that microorganisms can potentially play in improving both. Microbiome exploration has been able to identify and characterize the core and associated species of the microbial communities present in the different organs of tilapia. Aside from the host microbiota, microbial communities in the rearing environment have also been found to influence fish health. This review summarizes the studies that determined the core constituents of the microbiomes in the different organs (skin, gills, mouth and gut) in tilapia. In addition, research that has characterized the microbiomes of tilapia’s rearing environment; water, sediment and tank surfaces, are also reviewed. However, despite tilapia microbiome research to date, interactions between tilapia and its associated microbial communities remain poorly understood. A better understanding of how these microorganisms impact tilapia can potentially lead to better managing microbiomes to improve tilapia health and productivity. This review also sheds light on the different factors that influence tilapia microbiomes including their developmental stage, organ tissues and type of culture systems. The effects of on-farm practices such as diet, feeding regimes, use of probiotics, prebiotics, synbiotics, antibiotics, disinfection, and pond fertilization on tilapia microbiome were also investigated and summarized. By putting microbes in the spotlight, this review determined both the current status and knowledge gaps in tilapia microbiome research. This work identified critical, future research needs that can support the development of a deeper understanding of the link between microbiomes, tilapia health and productivity. In the future, harnessing microbiome-based management protocols will lead to enhanced, next generation tilapia best management practices, with major economic benefits.