We have recently reported the map positions of the ribosomal RNA genes and 6 protein-coding genes on the 292 kbp Chlamydomonas moewusii chloroplast genome. In the present study we localized 12 additional protein-coding genes on this green algal genome as well as 5 of these genes on the 196 kbp C. reinhardtii chloroplast genome. The gene mapping data agree with previous reports indicating that these two algal genomes differ tremendously in their global sequence organization and bear little similarity to their land plant counterparts. Among the 18 protein-coding genes examined, atpA and atpF of C. moewusii constitute the unique set of closely linked genes which is shared with land plant chloroplast genomes. The important gene order differences between the C. moewusii and C. reinhardtii chloroplast DNAs led us to speculate that gene grouping into transcription units is less prevalent in green algal chloroplast genomes than in their land plant homologs. To gain an insight into the transcriptional organization of the C. moewusii chloroplast genome, we probed Northern blots of total cellular RNA with clones covering 85% of this genome. Most chloroplast DNA regions were found to produce simple transcript patterns with RNAs less than 3.5 kb in size. This may be interpreted as indicating that Chlamydomonas chloroplast genes are transcribed mainly as monocistronic RNAs or that the RNAs observed are processed forms of unstable polycistronic transcripts.