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We isolated and characterized an oleaginous Thraustochytrid microalga. Based on 18 s rRNA sequencing, we classified this strain as Schizochytrium sp. SH103. Growth of these cells in a 5 L fermentor with a microbubble-type sparger (MTS) efficiently increased the oxygen transfer coefficient (OTC), while inducing only low external stress. For fermentation under conditions of low agitation (100 rpm) and aeration (3 L/min), the OTC was 8.6-fold higher using a MTS than a general type sparger (GTS). Under these same conditions, dry cell weight (DCW) productivity (0.54 vs. 1.26 g/L·h) and total lipid productivity (0.29 vs. 0.61 g/L·h) were each about 2.2-fold higher using a MTS than a GTS. Under conditions that optimized the OTC in a MTS fermentor (876 h−1), DCW productivity, total lipid productivity and DHA productivity were each 1.3-fold greater than non-optimized condition. Fed-batch fermentation experiments indicated the maximal DCW was 100.6 g/L at 48 h, maximal DCW productivity was 2.1 g/L·h, maximal lipid content was 48.6 g/L at 48 h, and lipid productivity was 1.0 g/L·h. Additionally, the results of experiments using a 50 L MTS fermentor (96.0 g/L DCW and 44.3 g/L total lipids at 48 h) were similar to those using the 5 L fermentor. Our results suggest that use of a MTS may help to achieve the efficient fermentation of heterotrophic microalgae for high cell densities.