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This chapter presents nitrogen assimilation in the context of genome analysis and gene function, with particular emphasis on inorganic nitrogen transporters, molybdenum cofactor (Moco) metabolism, and regulation of the nitrate assimilation pathway. In a comparative view, if considering only nitrate assimilation genes, Chlamydomonas and Arabidopsis show similar complexity whereas Ostreococcus, another unicellular alga, is much simpler. Understanding the bases of these differences will provide important perspectives into the biology of this pathway. Little information apart from that reviewed previously has been generated on the assimilation of organic nitrogen compounds in Chlamydomonas. A general view of the pathways is presented here, along with the putative genes involved. Glutamate is a key molecule that couples the metabolic pathways of amino acids with those of carbohydrates …