A total of 33 tropical thraustochytrid isolates were isolated from fallen leaves of Malaysian mangroves. Phylogenetic analysis based on the 18S rRNA gene revealed that the majority of the 33 isolates belonged to the genus Aurantiochytrium , and only one isolate belonged to Parietichytrium . The specific growth rate and biomass productivity of the strains ranged from 0.17 to 0.93 day −1 and 0.03 to 0.62 g l −1 day −1 , respectively. Lipid productivity ranged from 1.27 to 70.86 mg l −1 day −1 . Fifteen fatty acids, dominated by C16:0 [19.5%–71.6% total fatty acid (TFA)], C15:0 (3.3%–43.1% TFA), C22:6n3 (1.5%–38.4% TFA) and C18:0 (2.9%–28.6% TFA), were identified. The total carotenoid content was shown to be a better chemotaxonomic character than fatty acid composition for the isolates. Aurantiochytrium sp. UMACC-T024 had the highest lipid productivity (70.86 mg l −1 day −1 ), and this was selected for an optimisation study. The optimal conditions for lipid production of Aurantiochytrium sp. UMACC-T024 were salinity 32, pH 7.5, 1% w/v glucose and 0.5 g l −1 yeast extract, which resulted in an enhanced lipid productivity of 263.37 mg l −1 day −1 at day 5.