Abstract: The biosynthesis of lipids and carotenoids during the Schizochytrium ATCC20888 fermentation was investigated in this study using glucose and glycerol as single carbon source,separately. The results showed glucose benefited cell growth more than glycerol while glycerol fermentation was better for the accumulation of lipid especially of DHA.Besides,it showed Different content and composition of carotenoids were observed between the different carbon sources.After 7 days fermentation,the content of β- carotene when used glycerol as carbon source was 3.25 folds of that used glucose,while the content of lycopene and astaxanthin of the latter were 0.60 and 1.81 times higher than the former.There was a positive correlation between the carotenoids content and PKS products during the turnover stage with both carbon source,which indicated that carotenoids might play an important role in increasing the stability of the PUFAs in cells.