The frxC gene, found in liverwort chloroplast DNA, encodes a protein of unknown function. The deduced amino acid sequence of the protein shows significant homology to that of nitrogenase Fe-protein encoded by the nifH gene. We have cloned the frxC and nifH genes from the nitrogen-fixing cyanobacterium Plectonema boryanum, using frxC- and nifH-specific probes, and have determined their nucleotide sequences. The amino acid sequence deduced from the frxC gene of P. boryanum exhibits 83% homology to that of the protein encoded by the frxC gene from liverwort, whereas it exhibits only 34% homology to that encoded by the nifH gene from the same organism, namely, P. boryanum. Northern blot analysis showed that the frxC gene was transcribed more actively under nitrogenase-repressed conditions than under nitrogenase-induced conditions, suggesting that the FrxC protein has a function distinct from nitrogen fixation. These results, together with the phylogenetic relationship between the nifH and frxC genes, indicate that the frxC and nifH genes are derived from a common ancestral gene but have evolved independently to encode proteins with different functions.