The relationship between morphology of Schizochytrium sp. BCC 25505 and 25509 and production of docosahexaenoic (DHA) were studied in batch and pulsed-batch processes in optimized medium. In batch cultivation, the highest production by Schizochytrium sp. BCC 25505 (60-100% vegetative cells for 72 h) of biomass, DHA,  and total fatty acid were 38.7 ± 0.14 g/L at 72 h, 5.9 ± 1.56 g/L at 63 h, and 13.03 ± 0.09 g/L at 54 h, respectively, whereas that of  Schizochytrium sp. BCC 25509 (70-100% vegetative cells for 72 h) were 41.35 ± 0.46 g/L at 72 h, 12.09 ± 0.81 g/L at 69 h, and  26.32 ± 2.28 g/L at 66 h. In pulsed-batch cultivation, the highest production by Schizochytrium sp. BCC 25505 (57-86% vegetative cells) of biomass, DHA, and total fatty acid were 97.05 ± 1.63 g/L at 166 h, 20.73 ± 1.21 at 166 h, and 35.24 ± 3.27 g/L at 166 h, respectively, whereas that of Schizochytrium sp. BCC 25509 (25-94% vegetative cells) were 101.75 ± 2.19 g/L at 166 h, 20.0 ± 1.31 g/L at 143 h, and 36.48 ± 3.97 g/L at 118 h, respectively. Synchronous vegetative growth in high nitrogen content medium and in controlled high glucose supply for lipid accumulation enhanced efficiency of DHA production.