Microalgae have been studied for decades, but a new wave of research has recently begun as part of the search for renewable and sustainable energy sources. For economic optimization, microalgal biomass is being considered as a whole (main products and co-products) in an overall 'biorefinery' concept Applications of microalgae cover a broad spectrum, including the food and (livestock) feed industries, bio-energy, cosmetics, healthcare and environmental restoration or protection. In the field of biotechnology, the access to genomic data is playing a growing role. As the cost of sequencing strategies has fallen, studies of gene function at the transcript, protein and biosynthesis pathway levels have multiplied. Notably, sequencing and mass spectrometry technologies are used to delineate the pathways of lipid synthesis, which will be valuable for the future application of microalgae in the biotechnology and biofuel industries. Another field making an applied use of genomics is the 'cell factory' approach, which uses the cell to manufacture (express) natural or recombinant proteins for diverse purposes. In this chapter, we present a vision of the potential future of genomics in the biotechnology of microalgae from several points of view.