Water-oxidizing, phototrophic microorganisms have among the highest photosynthetic conversion efficiencies reported, can grow in diverse environments, such as salt water and industrial waste streams, synthesize a broad portfolio of biological energy carriers, and do not accumulate large quantities of recalcitrant biomass, such as lignin and cellulose. The three predominant products synthesized by phototrophic organisms include lipids, carbohydrates and proteins, each of which is relevant to bioenergy production. Lipids may be converted into diesel fuel surrogates, whereas sugars/starches and proteins can be metabolized into ethanol, butanol, H₂, and/or methane. However, significant challenges remain prior to using microalgae in an economically viable biofuel process. Metabolic carbon fluxes in algae are not currently optimized for anthropologic energy production. Carbon is partitioned between the two predominate energy storage molecules, starch and lipids, because they share a common metabolic precursor. Despite the significance of these molecules in algal physiology and for biofuel applications, the metabolic, enzymatic, and regulatory mechanisms controlling the partitioning of metabolites into these distinct carbon stores are poorly understood in algae. Research efforts have historically focused on manipulating lipid metabolism to increase lipid yields, but we have shown that alterations in carbohydrate metabolism can have a profound effect on carbon partitioning. Our research efforts show that when starch synthesizing enzymes are disrupted in the green alga Chlamydomonas reinhardtii a starch-less phenotype results with increased lipid content. Distinct starch-less algal mutants have unique effects on lipid and carbohydrate metabolism, and are excellent platforms for examining metabolic flux into lipid biosynthetic pathways.