The chloroplast genome of algae and plants typically comprises a circular DNA molecule of 100–200 kb, which harbours ∼120 genes, and is present in 50–100 copies per chloroplast. However, in peridinin dinoflagellates, an ecologically important group of unicellular algae, the chloroplast genome is fragmented into plasmid-like ‘minicircles’, each of 2–3 kb. Furthermore, the chloroplast gene content of dinoflagellates is dramatically reduced. Only 14 genes have been found on dinoflagellate minicircles, and recent evidence from EST studies suggests that most of the genes typically located in the chloroplast in other algae and plants are located in the nucleus. In this study, Southern blot analysis was used to estimate the copy number per cell of a variety of minicircles during different growth stages in the dinoflagellate Amphidinium operculatum. It was found that minicircle copy number is low during the exponential growth stage but increases during the later growth phase to resemble the situation seen in other plants and algae. The control of minicircle replication is discussed in the light of these findings.