The rpN5, rpl20, rplS. rps8, and a portion of the rp16 genes of the cyanelle genome of Cyanophora paradoxa have been cloned, mapped and sequenced. Homologs of the rpl35, rpi5, and rp16 genes are not found in the chloroplasts of higher plants. The rpi35 and rpf2@ genes most likely form a dicistronic operon which is located upstream from the apeE-apcA-apeE locus of the cyanelle and which is divergently transcribed from this locus. The rpfJ, rpl8, and rpl6 genes probably form a part of a larger cluster of genes encoding components of the cyanellar ribosomes. These genes are organized in a fashion similar to that observed in all procaryotes examined to date, with the exception that the rpsI4 p;ene is not found between the rpi5 and rps8 coding sequences. Hypotheses concerning the origins of cyanelles and chloroplasts are discussed.