The dinoflagellate chloroplast genome is fragmented into a number of plasmid-like minicircles, mostly containing one or more genes, and with a conserved core. We show here that, in addition to the transcripts of similar sizes to individual genes that have been reported previously, there are larger transcripts beginning and ending close to the core region. These may give rise to the smaller transcripts by processing. We also show that previously reported ORFs (open reading frames) are represented by transcripts that are significantly more abundant than those for non-coding regions, indicating that the ORFs are indeed functional. We show that 'empty' minicircles are also transcribed. We propose a model for linkage of DNA replication and transcription in dinoflagellate chloroplasts.