Chloroplasts originated from a cyanobacterium, which was engulfed by a primitive eukaryotic host cell. During evolution, chloroplasts have largely lost their autonomy due to the loss of many genes from their own genomes. Consequently, expression of genes encoded in the chloroplast genome is mainly controlled by the factors transferred from the cytosol to chloroplasts. However, chloroplast genomes of glaucophytes and red algae have retained some transcription factors (hypothetical chloroplast open reading frame 27 to 30 [Ycf27-Ycf30]) that are absent from green algae and land plants. Here, we show that the red algal chloroplast up-regulates transcription of the Rubisco operon rbcLS-cbbX via Ycf30 independently of nuclear control. Light-induced transcriptional activation of the Rubisco operon was observed in chloroplasts isolated from the red alga Cyanidioschyzon merolae. The activation was suppressed by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. These results suggest that chloroplast autonomously regulates transcription of the Rubisco operon in response to the activation of photosynthesis driven by the light. Transcriptional activation of the Rubisco operon was specifically repressed by the addition of anti-Ycf30 antibodies. Furthermore, reduced NADP, ribulose-1,5-bisphosphate, and 3-phosphoglyceric acid triggered the up-regulation of Rubisco transcription in the dark, and the activation was dependent on Ycf30. Thus, red algal chloroplasts have retained a nucleus-independent transcriptional regulation of the Rubisco operon to respond to environmental changes. The autonomous system would have been necessary for the initial fixation of cyanobacterial photosynthesis in the ancient nonphotosynthetic eukaryotic host. It has remained functional in the red algal chloroplast over evolutionary time.