Sequence similarities of proteins associated with plastocyanin-ferredoxin oxidoreduction (PcFdOR) activity of Photosystem I (PSI) were grouped and compared. PsaA, psaB, psaC, and petG represent genes that have been retained in the chloroplasts of both green- and red-lineage species. PsaD, psaE, psaF, and petF represent genes that have been retained in the chloroplast of red-lineage species, but have been transferred to the nuclear genome of green-lineage species. Translated sequences from red- and green-lineage proteins were compared to that of contemporary cyanobacteria, Synechocystis PCC 6803, and Gloeobacter violaceus PCC 7421. Within the green lineage, a lower level of sequence conservation coincided with gene transfer to the nuclear genome. Surprisingly, a similar pattern of sequence conservation existed for the same set of genes found in the red lineage even though all those genes were retained in their chloroplast genomes. This discrepancy between green and red lineage is discussed in terms of endosymbiotic gene transfer.