The gene (rbcL) for the large subunit (LSU) of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Cyanophora paradoxa was cloned and the nucleotide sequence determined. Sequence homologies to rbcL genes from other sources clearly indicated a close phylogenetic relationship between the photosynthetic organelles of Cyanophora (cyanelles), green chloroplasts and cyanobacteria. Our data support the hypothesis that the cyanelles of Cyanophora may represent a closely related, but independent, side line to chloroplast evolution. Cyanelles and rhodoplasts or phaeoplasts seem not to be related.