Dinoflagellates are a diverse and widely distributed protist group, of major environmental and economic importance. Many, but not all, are photosynthetic. Many of the photosynthetic species contain a secondary chloroplast of red algal origin with peridinin as an accessory pigment. These organisms have a highly anomalous chloroplast genome that is fragmented into plasmid-like molecules and highly reduced, encoding 12 proteins involved in photosynthetic light reactions as well as rRNA and some tRNAs. Chloroplast transcripts receive 3’ polyU tails, and many undergo RNA editing. Some lineages have replaced chloroplasts with others from non-dinoflagellate taxa, and in some instances the unusual processing pathways are applied to the newly acquired chloroplasts. Some non-photosynthetic lineages have lost chloroplast genomes, and others may have lost chloroplasts altogether.