Microorganisms play an important role in water quality maintenance, waste management, productivity enhancement, nutrient cycling, functional feed development, protection against infectious diseases, delivery of antigens and several other health benefits in aquaculture. The most significant use of microbes in aquaculture to minimize the antibiotics and drugs is through probiotics. The scope of probiotics in modern aquaculture has been enormous due to the detrimental consequences of routinely used antibiotics and chemotherapeutic agents and demand for safe aquatic products for human consumption. Since past few decades, both scientific and commercial interests are burgeoning in this field, and over the years, several probiotics are successfully used in aquaculture. Among various probiotics that are being used, Bacillus species are the common probiotics that are used in different aquatic animals. Several probiotics species belonging to Bacillus genus are currently been used, and Bacillus subtilis is one of such probiotics that is very well‐researched and most widely used probiotics in aquaculture. While its probiotic use has already been an important component in diverse aquaculture practices, its application in water quality improvement, utility in bioflocs/bioremediation and vehicle to express and delivery of heterologous antigen are noteworthy. It exerts innumerable beneficial effects such as improvement of growth, nutrition, immunity and disease resistance in aquatic species. This bacterium adopts a variety of disparate and overlapping mechanisms such as synergistic, antagonistic, competitive exclusion and immune‐stimulating effects. This review summarizes various applications of this bacterium as probiotics, bioremediating agent, bioflocing agent and possible live vaccine vehicle in aquaculture.