Cyanidioschyzon merolae is a unicellular alga with one chloroplast and one mitochondrion per cell. Each of these organelles has a simple nucleoid located in the central area. Prior to mitosis and cytokinesis, both the division of organelle nucleoids and organellokinesis occur simultaneously. We investigated the effects of nalidixic acid, an inhibitor of DNA gyrase, on the replication and division of organelle nucleoids. Using microfluorometry, we monitored the synthesis of organelle DNA (organelle S phase) in synchronous cultures. In both the chloroplast and the mitochondrion, DNA synthesis occurred from the start of the light period and ceased within 3 h. The addition of nalidixic acid at the start of the light period inhibited DNA synthesis in both organelles. Next, we added nalidixic acid to the synchronous culture at the beginning (just before the organelle S phase) or at the end (organelle G2 phase) of the light period and monitored the division of organelle nucleoids in the dark period. Approximately 50 to 70% of chloroplast nucleoids divided unequally in both experiments. Despite the unequal division of the chloroplast nucleoids, electron microscopy revealed that the chloroplasts were divided into equal daughter chloroplasts by the chloroplast-divided ring. During the same treatments, all of the mitochondrial nucleoids underwent normal and equal division. Our results suggest the involvement of DNA gyrase in the replication of chloroplast and mitochondrial DNA and in the division of the chloroplast nucleoid, as well as a difference in mechanism between the division of chloroplast and mitochondrial nucleoids.