In order to develop a reliable and highly productive large-scale culture process for microalgae and high value products from microalgae, a good understanding of algal physiology and metabolism is essential. This is important in the process of strain selection and also in the optimisation of culture conditions and for culture management. Recent new developments in genome scale metabolic reconstruction and metabolic flux analysis (Boyle and Morgan 2009; Chang et al. 2011; de Oliveira Dal’Molin et al. 2011) and analysis of gene expression (e.g., Lei et al. 2012; Valenzuela et al. 2012) are providing new tools for analysing the complex metabolic interactions in algae and should aid in the optimisation of cultures for the production of specific products of interest as well as in developing genetic engineering strategies to improve algae strains.