The applications of Omega-3 fatty acids for human health are rapidly expanding, which necessitates exploring alternative sources to fish. Many marine microorganisms across different kingdoms exhibit the ability to store a significant oil content, however are difficult to cultivate. Out of all marine microbes, thraustochytrids are considered a good source for the production of high value compounds such as polyunsaturated fatty acids (PUFAs). Optimization of culture conditions will be helpful in further enhancing cellular lipid content to suit fatty acid synthesis. This chapter describes some recent advances in the development of marine microbes for fatty acid production with a special emphasis upon thraustochytrids for biotechnological applications, focussing particularly on methods to enhanced docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) production.