At present we are also studying the remodeling of Chlamydomonas metabolism after transition to anaerobic growth conditions. The versatile metabolism of the green alga Chlamydomonas reinhardtii is reflected in its ability to acclimate to anaerobic conditions. The complex anaerobic response is also remarkable in the context of renewable energy since C. reinhardtii is able to produce hydrogen under anaerobic conditions. To identify proteins involved during anaerobic acclimation as well as to localize proteins and pathways to the powerhouses of the cell, chloroplasts and mitochondria from C. reinhardtii in aerobic and anaerobic (induced by 8 hours of argon bubbling) conditions were isolated and analyzed using comparative proteomics. A total of 2315 proteins were identified. Further analysis based on spectral counting localized 895 of these proteins to the chloroplast, including many proteins of the fermentative metabolism. Comparative quantitative analyses were performed with the chloroplast-localized proteins using stable isotopic labeling of amino acids (13C6 Arginine/12C6 Arginine in an Arginine-auxotrophic strain). The quantitative data confirmed proteins previously characterized as induced at the transcript level as well as identifying several new proteins of unknown function induced under anaerobic conditions. These proteins of unknown function provide new candidates for further investigations taking advantage of reverse genetics. An important aim hereby is to understand the anaerobic response in the green alga. Another important aim will be to engineer Chlamydomonas strains that produce hydrogen in amounts allowing commercial exploration of the process.