This book opens with a review suggesting that transgenic Nannochloropsis microalgae have a broad spectrum of applications in marine and plant biotechnology and that have the propensity to be a source of raw material for a wide range of industries. The authors express this while going on to present an overview of the future uses of this genus in the context of genetic improvement for new biotechnological applications. The provision of nitrogen from different sources is presented as a strategy used to modify the biomass composition. Nitrate is the ideal nitrogen source and gives the highest biomass concentration and specific growth rate when compared with urea and ammonium. Additionally, modern advancements in the application of Nannochloropsis biomass for commodity chemicals, feeds, high value products, biofuels, cosmetics, fertilisers, and materials production are presented, in conjunction with challenges and future perspectives in the utilisation of Nannochloropsis biomass for biorefinery development in microalgae-based industries. The characteristic of Nannochloropsis oculata are described using an integrated biorefinery approach based on palm oil milling as a model system. Subjects addressed include the bioengineering aspects for the conversion of light into biomass, co-location strategy to take advantages of the industrial wastes of energy, water and nutrients, productivities of the different reactor systems and configuration, use of palm oil mill effluent (POME) as a substitute source of nutrients, biomaterials co-utilisation, bioenergy co-generation, downstream processing aspects for extraction, purification and conversion into value-added products for pharmaceuticals and functional foods. Continuing, common methods for characterisation of βG from diatom and non-diatoms microalgae are described to conclude that Nannochloropsis (particularly NpUNAM) has significant potential for the industrialised production of βG. Lastly, the extraction of cytoplasmic soluble proteins is depicted as one of the challenges for effective development of microalgae biotechnological potential, with correctly selected Pulsed Electric Fields resulting in the release of cytoplasmic soluble proteins.