[Objective] To produce drug resistance, seek non-toxic environmental so as to change the current biological drugs that did not excessive use of antibiotics. [Methods] A strain of Bacillus was purified and isolated from fresh and healthy in- testines of grass carps. Biochemical identification was carried out by conventional bacterial biochemical test method. Two pairs of primers were designed, 16S rRNA detection and sequencing analysis were carried out. Drug sensitive test was carried out by agar diffusion method. In vitro inhibition test on Staphylococcus aureus was carried out by Oxford cup method. [Results] The isolated bacterium had basically the same biochemical characters as Bacillus subtilis; and the homology reached 100%. Thus, the isolated bacterium was identified to be Bacillus subtilis. It was insensitive to amoxicillin, ampicillin, penicillin G and so on, but sensitive to amikacin, cefalexin, ciprofloxacin and cefradine. The inhibitory effects of Bacillus subtilis on Staphylococ- cus aureus were significant. The minimum inhibitory concentration (MIC) was 2.8×10^8×2^-5/ml and minimum bactericidal concentration (MBC) was 2.8×10^8×2^-2/ml. [Conclusions] The isolated Bacillus subtilis could be used to prevent and control diseases caused by Staphylococcus aureus, and reduce the abuse of antibiotics.