There has been growing interest in microalgal cultivation to produce high value compounds with potential applications in human health, livestock, aquaculture and biofuels. Compounds derived from triglycerides and lipids in microalgae are of particular interest as these substances can comprise 20-70% of the dry mass of the organism. However, due to high costs involved in lipid downstream processing, biorefinery platforms typically produce other important co-products such as polysaccharides, proteins, terpenes, phenolics and alkaloids to offset the oil production costs. For lipid-intensive production, single cell oils from cultured microalgae are of particular interest as they offer an alternative to plant-based lipids that require land use. In this context, heterotrophic thraustochytrids could be a potential source of useful tryglycerides and due to their amenability to the tuning of the oil profile through various fermentation and metabolic influences. In this way, these organisms can be engineered to produce the fatty oil profile of plant oils. Furthermore, thraustochytrids can produce high value nutritional oil containing omega-3 fatty acids, such as docosahexaenoic acid (DHA) mainly in the form of triglycerides. Remarkably, triglycerides accumulated in thraustochytrids constitute more than 90% of the lipids, which can be used as high value nutritional supplements for humans. In addition, low cholesterol content makes thraustochytrid oil desirable for supplementing food products. Thraustochytrid derived-oil has been designated 'generally recognized as safe' status for its use in food products. In other applications, thraustochytrid oil containing triglycerides has been produced as a precursor for biodiesel production.