Groupers are an important mariculture fish in Taiwan and Southeast Asian countries. The rapidly growing orange spotted grouper (Epinephelus coioides) has experienced relatively severe bacterial disease problems. The proliferation of pathogens in fish can be suppressed by commensal microbiota. In this context, probiotic seem to offer an attractive alternative. Bacillus subtilisis a probiotic bacteriumthat is administered in diet to suppress proliferation of pathogens. In the present study, E.coioideswere fed for 6 months with diets containing B.subtilis at 0 (control), 0.1 % and 1 %. Percent weight gain and feed efficiency of the 0.1 and 1 % groups were significantlybetter than the control group. The innate cellular response, respiratory burst of the fish fed the 1 % and 0.1 % diet was significantly higher compared to the control group on 10 or 20 days after feeding, and even moresignificanton 30 days.ProbioticBacillus subtilis increased the fish¡¦s intestinal microbial diversity as measured by visible band number and Shannon diversity indexin DGGE analysis. Probiotic Bacillus subtilis also stimulated the population of bacterial species likePaenibacillussp,Lactobacillus oenistrain 59 b, and Methilacidophiluminfernorumstrain V4 that beneficial for Epinephelus coioides. The best dose of probiotic Bacillus subtilis based on growth performances, innate cellular responses and profile of microbiota in fish intestines is 0.1 %, which showed equal efficacy as the 1% diet.