Microalgae are considered promising cell factories to produce various types of biofuels, including bioethanol, biodiesel, and biohydrogen, by using carbon dioxide and sunlight. Despite the unique advantages of these microorganisms, the commercialization of microalgal biofuels has been hindered by unfavorable economic factors. Metabolic engineering is among the most promising strategies put forth to overcome this challenge. In this chapter, metabolic pathways involved in lipid and hydrogen production by microalgae are reviewed and discussed. Moreover, metabolic and genetic engineering approaches investigated for improving the rate of lipid production (as a feedstock for biodiesel production) and biohydrogen synthesis are presented. Finally, genetic engineering tools and approaches employed for engineering microalgal metabolic pathways are described in detail. A thorough step-by-step protocol for reconstructing the metabolic pathways of various microorganisms, including microalgae, is also presented.