Prochlorophytes are prokaryotes that carry out oxygenic photosynthesis using chlorophylls a and b, but lack phycobiliproteins as light-harvesting pigments. These characteristics distinguish them from cyanobacteria, which contain phycobiliproteins, but no chlorophyll b. Three prochlorophyte genera have been described: Prochloron, Prochlorothrix and Prochlorococcus. The prochlorophytes share their pigment characteristics with green plant and euglenoid chloroplasts, which has led to a debate on whether these chloroplasts may have arisen from an endosymbiotic prochlorophyte rather than a cyanobacterium. Molecular sequence data, including those presented here based on a fragment of the rpoC1 gene encoding a subunit of DNA-dependent RNA polymerase, indicate that the known prochlorophyte lineages do not include the direct ancestor of chloroplasts. We also show that the prochlorophytes are a highly diverged polyphyletic group. Thus the use of chlorophyll b as a light-harvesting pigment has developed independently several times in evolution. Similar conclusions have been reached in parallel studies using 16S ribosomal RNA sequences.