Adaptive laboratory evolution (ALE) is an effective method in changing the strain characteristics. Here, ALE with high oxygen as a selection pressure was applied to improve the production capacity of Schizochytrium sp. Results showed that cell dry weight (CDW) of endpoint strain was 32.4% higher than that of starting strain. But slight lipid accumulation impairment was observed. These major performance changes were accompanied with enhanced isocitrate dehydrogenase enzyme activity and reduced ATP: citrate lyase enzyme activity. And a serious decrease of 62.6% in S-DHA (140rpm -> 170rpm) was observed in the endpoint strain. To further study the docosahexaenoic acid (DHA) production ability of evolved strain, fed-batch strategy was applied and 84.34 g/L of cell dry weight and 26.40 g/L of DHA yield were observed. In addition, endpoint strain produced greatly less squalene than starting strain. This work demonstrated that ALE may be a promising tool in modifying microalga strains. (C) 2016 Elsevier Ltd. All rights reserved.