We constructed a plasmid probe containing DNA sequences unique for chloroplast (Cp) genome and nuclear genome of Chlamydomonas reinhardtii. Using this probe and quantitative Southern blot analyses, we determined the content ratio of Cp DNA/nuclear DNA in total DNA isolated from cells grown in different conditions. Algal cells grown photoheterotrophically with acetate as an added carbon source contain the highest amount of Cp DNA compared with cells grown in other conditions tested. We investigated the effect of nitrogen limitation, 5-fluorodeoxyuridine treatment, cadmium exposure, photoautotrophic growth, and heterotrophic growth in darkness. The change in the Cp/nuclear DNA ratio in cells shifted from one growth condition to another depended on cell division; Cp DNA content in undivided cells remained constant. Therefore, the reduction of Cp DNA content was attributed by under replication rather than selective degradation of Cp DNA. Cells with low Cp DNA content often contained less reduced glutathione, suggesting the possible effect of redox status. Low Cp DNA content was detected in cells treated with inhibitors that block electron flow of photosystems and in mutants with PS I defective phenotype. On the basis of these data, we propose that in C. reinhardtii, Cp DNA replication be modulated by redox status.