Abstract: This study aimed to investigate the biological effects induced by low energy ions implantation on neutral protease producing bacteria. A bacterium, Bacillus subtilis AS1.398，which could produce neutral protease was mutagenized by implanting 30 keV N⁺ ions beam and a highyield mutant strain ZC12 was obtained，And the activity of the mutant was 0.84 times more than the original strain. Mutagenic effects were investigated，and the results indicate that the survival rate curve takes a “saddle” shape and high positive mutation rate is occurred in this region，these show that unique mutation effects of ion implantation are presented. The DNA sequences of the neutral protease genes in the original strain and the mutant were cloned and analyzed. Through blasting this two CM(38sequences, five amino acid sites of mature peptide were changed showing that unique mutation effects of ion implantation were presented．As a result, low energy ions implantation was successful in neutral protease producing bacteria breeding.