The green unicellular alga Chlamydomonas reinhardtii has long been used as a model system for studying photosynthesis, chloroplast biogenesis, and flagellar function and assembly because of its well-defined genetics. The value of this organism has been greatly increased recently by the development of efficient methods for nuclear and chloroplast transformation. While homologous recombination appears to occur at a low frequency in the nuclear genome, random integrations can be exploited to tag genes of interest by insertional mutagenesis. Cloning of the nuclear genes by genomic complementation is also possible. Chloroplast genetic engineering has provided new and important insights into the molecular mechanisms of chloroplast gene expression and into the function of chloroplast proteins. C. reinhardtii is probably the best organism in which to perform chloroplast DNA surgery because of the ease of chloroplast transformation in this alga. C. reinhardtii might be described as the photosynthetic yeast. However, it offers additional new promising areas of research, such as chloroplast-mitochondrial interactions, phototransduction, and the behavioral response to light.