Microalgae are unicellular photo- and heterotrophic organisms that, being efficient producers of a rich and complex biomass, have attracted global interest as biofactories for the production of high-value compounds (e.g. PUFAs, proteins and pigments) that can find application in nutraceutical, pharmaceutical and food industries. Microalgae have also been extensively studied in the last two decades, as potential producers of biofuels. However, based on current technologies, this production process is not economically sustainable yet. In this frame, the recent advances in genomic and transcriptomic characterization of microalgae can represent the key to understand the metabolic mechanisms underlying the growth regulation and the biosynthesis of those valuable metabolites, in order to improve the use of microalgae as biofactories.