Eighteen strains of thraustochytrids were newly isolated from Hong Kong mangroves, and their fatty acid and squalene contents were analyzed. All strains could grow well heterotrophically with glucose as the sole carbon source. All of them had the typical fatty acid profile of thraustchytrids and could produce a large amount of docosahexaenoic acid. The cell dry weight ranged from 5.49 to 15.62 g/L and squalene content from 0.02 to 0.18 mg/g at 72 h. The highest squalene-producing strain, BR-MP4-A1 was identified as a new strain of Aurantiochytrium species through sequence comparison of the 18S rRNA gene. The highest biomass of Aurantiochytrium sp. BR-MP4-A1 was achieved at 72 h, whereas its squalene content reached the maximum of 0.567 mg/g at 36 h but decreased rapidly thereafter. The production of squalene by thraustochytrids might be highly influenced by culture conditions.