Preventing diseases in aquatic animals is of significant economic importance, since small fish have high mortality rates due to high incidences of disease, low water quality among others. Several years ago, the main treatment to protect fishes against different bacterial diseases in hatchery conditions were chemotherapeutic agents (antibiotics) or vaccination. The previous methods may change the profile of a healthy gut microflora, while the vaccination method can be stressful for fish; both methods can enable the access of some pathogens. The use of chemotherapeutic agents can also lead to resistant bacteria, and so their use should be restricted or at least controlled; and so, this study was conducted to investigate the effects of different amounts of probiotics on the water quality parameters in the culture of grouper fingerling (Epinephelus Coioides); species which has become one of the main cultured fish in Taiwan according to FAO. The effects of the probiotic, Bacillus subtilis, on grouper fingerling breeding and water quality was evaluated in this study by adding the probiotic to the feed. Two concentrations of probiotic were administered including 0.1%, 1.0% and the control. During the experiment, fingerling development, growth rate, survival rate and water quality parameters including ammonia-N and nitrite-N, total bacterial count, and presumptive Vibrio count were determined. The presumptive Vibrio count presented was significantly suppressed after Bacillus treatment.