Bioactive metabolites are certain metabolites that are synthesized inside cells or secreted in the extra-cellular environment, and they show certain activities on various sources which make them important compounds in biotechnology. Bioactive metabolites can be synthesized by using the tools available in industrial biotechnology or the recent techniques developed in genetic engineering. Microalgae have significant potential for the production of biomass and bioproducts, including lipids that can be transformed into biodiesel, long-chain polyunsaturated fatty acids for human health and high-value pigments with antioxidant properties. Most production processes are based on light-dependent assimilation of CO2. Genetic transformation is compartmentalized into three types of organelles: mitochondria, chloroplast and nucleus. The only microalga where the three genomes can be selectively transformed is the green microalga Chlamydomonas reinhardtii, where chloroplastic and mitochondrial genomes can be transformed using particle bombardment while the nuclear genome is transformed by electroporation or glass-bead agitation.