Decreasing fossil fuels and its impact on global warming led to an increasing demand for its replacement by sustainable renewable biofuels. Microalgae may offer a potential feedstock for renewable biofuels capable of converting atmospheric CO2 to substantial biomass and valuable biofuels, which is of great importance for the food and energy industries. Integrated “Omics” Research is a powerful tool in understanding the behavior of biological systems as a whole, where the metabolic pathways are often highly regulated and connected with a number of both feedforward and feedback mechanisms that can act positively and/or negatively ultimately affecting the systems output. Understanding the entire system through Integrated “Omics” Research will lead to identify relevant enzyme-encoding genes, and reconstruct the metabolic pathways involved in the biosynthesis and degradation of precursor molecules that may have potential for biofuel production, aiming towards the vision of tomorrow’s bioenergy needs.