In maize (Zea mays L.), four ferredoxin (Fd) isoproteins, Fd I to Fd IV, are differentially distributed in photosynthetic and nonphotosynthetic organs of young seedlings (Y Kimata, T Hase [1989] Plant Physiol 89: 1193-1197). To understand structural characteristics of the Fd isoproteins and molecular mechanism of the differential expression of their genes, we have cloned and characterized three different maize Fd cDNAs. DNA sequence analyses showed that two of the cDNAs encoded the entire precursor polypeptides of Fd I and Fd III, which were composed of 150 and 152 amino acid residues, respectively, and the other encoded a 135 amino acid precursor polypeptide of Fd not yet identified. High degrees of homologies were found in the deduced amino acid sequences of mature regions of these Fd isoproteins, but the transit peptide of Fd III differed considerably from those of other Fd isoproteins. Fd I and the unidentified Fd were encoded mainly with codons ending in C or G, but such strong codon bias was not seen in Fd III. Gene specific probes for each cDNA were used to probe Northern blots of RNA isolated from leaves, mesocotyls, and roots of maize seedlings. The gene transcripts for Fd I and the unidentified Fd were restricted to leaves and their levels increased markedly upon illumination of etiolated seedlings, whereas that for Fd III was detected in all organs and its accumulation was not light dependent. This organ specific accumulation of Fd mRNAs corresponds exactly to the distribution pattern of Fd isoproteins.