In the isogamous green alga Chlamydomonas reinhardtii, the chloroplast genome is transmitted from the mt+ parent, while the mitochondrial genes are believed to be inherited from the mt- parent. Chloroplast nucleoids have been visualized by DAPI (4,6-diamidino-2-phenylindole) staining, and the preferential digestion of the mt- chloroplast nucleoids has been observed in young zygotes. However, the mitochondrial nucleoids have never been visualized, and their behavior is only deduced from genetic and biochemical studies. We discovered that the mitochondrial and chloroplast genomes can be visualized simultaneously in living cells, using the fluorescent dye SYBR Green I. The ability to visualize the mitochondrial and chloroplast genome in vivo permits the direct observation of the number, distribution and behavior of the chloroplast and mitochondrial nucleoids in young zygotes. Using this method, the biparental transmission of the mitochondrial genome was revealed.