Bacillus as spore-forming bacteria are resistant to aggressive physico-chemical conditions showing unusual physiological characteristics that enabling them to survive under different environmental conditions such as fresh waters, marine sediments, desert sands, hot springs, and the gastrointestinal tract of finfish and shellfish. Bacillus bacteria can rapidly replicate and tolerate a multitude of environmental conditions, giving a wide range of beneficial effects in the aquaculture sector. Application of Bacillus bacteria as probiotics in feed or as bioremediatory agents of aquaculture rearing water has great potential for a sustainable aquaculture. Removal of waste products from water column, maintaining optimum water quality, and reducing stress, are parts of bacilli probiotics in aquaculture with an outcome of balancing and or enhancing of animal immuno-physiological variables and a higher aquaculture production. Probiotic bacilli can also reduce the load of pathogenic microorganisms but maintaining a higher density of beneficial bacteria in aquaculture systems. It is, however, important to know how the probiotic bacilli efficacy and potency can be affected by aquatic animal species and age, water quality and diet as well as details of bacilli mode of actions on the immune-physiological functions of aquatic animals. Also, with an increase in the potential pathogenic bacilli, their applications in form of probiotic in aquaculture required more attention. This presentation discusses the various effects of probiotics bacilli in aquaculture and future research work required.