The use of Omega-3 fatty acids is garnering increasing interest due to its substantial effects on human health. Fish are a major dietary source of ω3FA; however, they are not the primary producers. The primary producers are microalgae and other microorganisms, which serve as the original source of omega-3s in the food chain. The marine fish, however, has not been able to meet the global demands. Recently, the generation of fatty acids has been investigated from another source, namely microorganisms. Omega-3 fatty acids are naturally produced by the microorganisms. However, the use of metabolic engineering has provided evidence for improvements in production. The current article reviews research on microorganisms using engineering ways to accumulate ω3FA such as docosahexaenoic acid or DHA and eicosapentaenoic acid or EPA. These studies have demonstrated that modulation of existing pathways, as well as reconstitution of biosynthetic pathways, has a high potential for increasing the fatty acid yield. However, certain bottlenecks limit the yield of fatty acids in various host organisms. These may include the fatty acid flux of intermediates that exists between various lipid pools. Even though the heterologous and native microbes show fatty acid flux under acyltransferases control, there is evidence that modulation of even a single acyltransferase by genetic approach can provide significant alteration for producing fatty acids. The microbes with oleaginous properties are being identified rigorously and are expected to further advance the process of engineering which leads to enhanced production of fatty acids in microbes.