We show using PCR that psbC, atpA and petB genes are present in the plastid DNA minicircles from the dinoflagellate Amphidinium operculatum, extending the set of plastid genes identified from this organism. Unusually, the petB and atpA genes are located on the same minicircle. PCR using primers based on the "core" region found on all coding minicircles revealed the existence of a number of DNA minicircles with no apparent coding function. Northern analysis of total RNA from A. operculatum showed that the petB and atpA genes are represented on separate transcripts, despite being encoded in close proximity on the same minicircle. The possibility of transcript editing was investigated by RT-PCR, but psaA, psbA, psbB and atpB transcripts showed no evidence of editing, indicating that GUA can be used as an initiation codon in A. operculatum.