Summary:To determine the exact mode of inheritance of mitochondrial DNA (mtDNA) in Chlamydomonas reinhardtii, suitable markers to determine the origin of parental mitochondrial genes are necessary. For this goal, the difference in mtDNA between a C. reinhardtii strain and a C. smithii strain was used. These two species were serially backcrossed to ensure matching of the background of their nuclear genomes. The results showed strict paternal inheritance of mtDNA. Next, the fate of mt + (female) and mt -(male) mtDNA was followed using three methods: quantitative real-time PCR, Southern blotting hybridization, and fluorescence in situ hybridization (FISH). The disappearance of mt + mtDNA was observed at the beginning of meiosis. In the mutant bp31, in which the maternal inheritance of chloroplast DNA (cpDNA) is disrupted, the paternal inheritance of mtDNA was also found to be disrupted, indicating commonality between cpDNA and mtDNA in part of the process leading to uniparental inheritance. Mitochondrial nucleoids and mitochondria were observed in living vegetative cells. Organellar nucleoids were stained with SYBR Green I, while mitochondria were stained with DiOC6. During the cell cycle, mitochondrial nucleoids in living cells were granular, and mitochondria formed tangled threads. When mature zygotes were exposed to the light, meiosis began. Living zygotes with thick walls was also stained by SYBR Green I and DiOC6. At the diakinesis stage of meiosis, the total number of chromosomes was 18. When mature zygotes were exposed to the light, granular mitochondria began to form short thread-like structures and then assembled around the cell nucleus. Once assembled, the mitochondria began to scatter in the opposite hemisphere, forming long and tangled thread-like structures. Mitochondrial nucleoids were usually granular, but some of them developed bead-like structures, probably by dividing. The results from the molecular biochemical experiments suggested that mt + mitochondrial nucleoids disappear at the stage of assembly and the scattering of mitochondria. Then, the first and second nuclear divisions proceed, producing tetrads.