Algae and other marine organisms are responsible for the fixation of almost half of all inorganic carbon in the atmosphere. This could lead to the production of inexpensive bulk chemicals by autotrophic organisms, such as algae, because energy provided by sunlight and the carbon source are essentially free. Compared to higher plants, the metabolic pathways in algae can be more easily manipulated because of the wealth of knowledge and genetic tools available. Algae also grow faster which results in shorter development times for metabolically engineered strains. In order to engineer algae to produce chemicals, one must first gain a fundamental understanding of flux distribution within different pathways as well as in different cellular compartments. Prerequisite for experimental determination of metabolic fluxes is a stoichiometric model. We have constructed a stoichiometric model of C. reinhardtii from genomic analysis and the scientific literature. To our knowledge, it is the most comprehensive stoichiometric metabolic model in algae including the reactions of glycolysis, citric acid cycle, oxidative and reductive pentose phosphate cycles, and starch and amino acid synthesis pathways. Our model also accounts for the transport and reactions of metabolites that occur in the major subcellular compartments, the chloroplast and the mitochondria. Biomass composition (lipid, carbohydrate and protein compositions) and growth rate measurements are used to model the metabolic flux towards biomass. Under mixotrophic growth conditions, the uptake rate of acetate is measured and serves as an additional constraint on biomass synthesis. We will compare the differences in fluxes of a wild-type strain to a cell wall deficient mutant. A two step optimization will be used to solve the model with the first objective function being maximum growth subject to a fixed carbon input. The second step is to set the biomass flux and minimize light input. The flux maps for the different growth regimes (mixotrophic and autotrophic) will be constructed and compared against results from the prokaryotic phototroph, Synechocystis sp. PCC6803.