Schizochytrium sp. is a hopeful docosahexaenoic acid (DHA) producing candidate due to its rapid growth rate and high DHA proportion in total lipid content. In this study, low-energy ion implantation was applied to Schizochytrium sp. to induce high DHA-producing mutants. Screening these mutants by Sudan black B staining, a mutant strain S1 which showed a 61% improvement in DHA production than that of the parent strain was successfully selected. Subsequently, parameters of DHA production of mutant strain S1 were optimized in a 500-mL Erlenmeyer flask. Under the optimum fermentation conditions, the production of DHA and the percentage of DHA in total lipid of mutant strain S1 were 6.52 g/L and 46.2%, respectively. This study provides an effective breeding strategy for improved DHA production of Schizochytrium sp. through combination of the novel mutagenesis technology, the effective screening method and fermentation optimization. (C) 2016 Elsevier Ltd. All rights reserved.