In the present study, a novel oleaginous Thraustochytrid containing a high content of docosahexaenoic acid (DHA) was isolated from a mangrove ecosystem in Malaysia. The strain identified as an Aurantiochytrium sp. by 18S rRNA sequencing and named KRS101 used various carbon and nitrogen sources, indicating metabolic versatility. Optimal culture conditions, thus maximizing cell growth, and high levels of lipid and DHA production, were attained using glucose (60 g l(-1)) as carbon source, corn steep solid (10 g l(-1)) as nitrogen source, and sea salt (15 g l(-1)). The highest biomass, lipid, and DHA production of KRS101 upon fed-batch fermentation were 50.2 g l(-1) (16.7 g l(-1) day(-1)), 21.8 g l(-1) (44% DCW), and 8.8 g l(-1) (40% TFA), respectively. Similar values were obtained when a cheap substrate like molasses, rather than glucose, was used as the carbon source (DCW of 52.44 g l(-1), lipid and DHA levels of 20.2 and 8.83 g l(-1), respectively), indicating that production of microbial oils containing high levels of DHA can be produced economically when the novel strain is used.