Background Chitosan hydrolysis by chitosanase is one of the most effective methods to produce chitosan oligosaccharides, however, the low yield of chitosanase cannot meet the current requirement. In this paper, a strain producing chitosanase was screened, and a novel mutagenesis system (1)) was selected to increase the yield of chitosanase. The hydrolyzed products from chitosan by chitosanase produced by mutan train were also analyzed by LC-MS. Results A strain of Bacillus cereus capable of producing chitosanase was screened and identified from soil samples. A mutant strain of Bacillus cereus was obtained by ARTP mutagenesis and bioscreening method, and chitosanase activity was 2.49 folds that of the original bacteria. After optimized fermentation conditions, the enzyme activity of the mutant strain was 3.3 folds that of the original bacteria. The relative molecular weight of the purified chitosanase was 43 kDa. Ten chitosan oligosaccharides(2–4 oligosaccharides) were obtained by hydrolyzing chitosan with it. Conclutions: The results showed that the ARTP mutagenesis and bioscreening method could significantly increase the yield of chitosanase in B. cereus, and had little effect on the properties of the enzyme. These findings have potential applications in mutagenesis of other enzyme-producing microorganisms.