The molecular function of mTERFs (mitochondrial transcription termination factors) has so far only been described for metazoan members of the protein family and in animals they control mitochondrial replication, transcription and translation. Cells of photosynthetic eukaryotes harbour chloroplasts and mitochondria, which are in an intense cross-talk that is vital for photosynthesis.Chlamydomonas reinhardtiiis a unicellular green alga widely used as a model organism for photosynthesis research and green biotechnology. Among the six nuclearC. reinhardtiimTERF genes is mTERF-like gene of Chlamydomonas (MOC1), whose inactivation alters mitorespiration and interestingly also light-acclimation processes in the chloroplast that favour the enhanced production of biohydrogen. We show here fromin vitrostudies that MOC1 binds specifically to a sequence within the mitochondrial rRNA-coding moduleS3, and that a knockout of MOC1 in the mutantstm6increases read-through transcription at this site, indicating that MOC1 acts as a transcription terminatorin vivo. Whereas the level of certain antisense RNA species is higher instm6, the amount of unprocessed mitochondrial sense transcripts is strongly reduced, demonstrating that a loss of MOC1 causes perturbed mitochondrial DNA (mtDNA) expression. Overall, we provide evidence for the existence of mitochondrial antisense RNAs inC. reinhardtiiand show that mTERF-mediated transcription termination is an evolutionary-conserved mechanism occurring in phototrophic protists and metazoans.