The heterotrophic marine microalga Schizochytrium mangrovei PQ6 synthesizes large amounts of polyunsaturated fatty acids (PUFAs) with possible food and fuel applications. We characterized the transcriptome of S. mangrovei PQ6, focusing on lipid metabolism pathways throughout growth. Maximum lipid accumulation in 500 mL batch cultures occurred on day 5, with total lipid and DHA contents reaching 33.20±1.25% of dry cell weight (DCW) and 135.91 mg/g of DCW, respectively. We identified 30,782 unigenes from the transcriptomes of samples collected on day 1, 3, and 5, with an average size of 672.7 bp and N50 of 950 bp. A total of 9,980 unigenes were annotated in public protein databases. We identified 155 unigenes involved in lipid metabolism whose expression patterns corresponded with total lipid and DHA accumulation patterns, shedding light on the possible roles of PUFA pathways, such as those mediated by fatty acid synthase, polyketide synthase, and desaturase/elongase, in Schizochytrium.