Thraustochytrids, a group of osmoheterotrophic marine protists, have recently gained increased attention owing to their spectacular biotechnological potentials. They possess enormous capability of producing omega-3 (omega-3) polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and several other bioactive metabolites, known to have nutritional implications in human health. They have emerged lately as an efficient economic alternative compared with other fish and algal oil sources by virtue of their simpler PUFA profiles and cost-effective culture conditions. This review is an attempt to summarize the ecological significance of thraustochytrids with an emphasis on their cultured and uncultured diversity from various marine habitats accounted during the last few decades. Moreover, improved technologies such as media optimization in conjugation with metabolic engineering, adopted for biotechnological advancement of omega-3 products of thraustochytrids are highlighted with particular concern on the respective fatty acid biosynthetic pathways. One of the future prospects focuses on utilization of thraustochytrids for biodiesel production owing to their tremendous potentiality of yielding low carbon monounsaturated fatty acids (LC-MUFAs). However, there is utmost need of in-depth diversity assessments from various oceanic ecosystems in order to gain insight on potential thraustochytrids for ameliorated employment toward biotechnological applications.