Neochrome (NEO) is a particular chimeric photoreceptor that can respond to red/far red as well as blue light. Using this photoreceptor, some cryptogams may enhance light sensitivity at low light environment. However, the NEO sequence information is extremely limited. Using inverse PCR and single oligonucleotide nested PCR genome-walking approaches, the full-length genomic sequences of NEO genes were determined for three fern species Coniogramme intermedia var. glabra, Plagiogyria distinctissima and Pronephrium lakhimpurnense. Sequence and structure analysis results indicate that they possess a conserved structure and organization. Introns are absent in three genes. They each contain an 4332, 4308 and 4317-bp ORF (Open reading frame), encoding a deduced protein with 1443, 1435 and 1438 amino acid residues. Their N-terminus consists of a putative functional phytochrome sensory module including PAS (Per / Arnt / Sim), GAF (cGMP specific phosphodiesterase / adenylate cyclases / formate hydrogen lyase transcription) and PHY (phytochrome) domains, whereas the C-terminus contains a nearly complete phototropin with two LOV (Light, Oxygen and Voltage-sensing) and one STKc (Serine/Threonine protein kinases, catalytic) domains. Phylogenetic analyses revealed that they are evolutionarily close to their homolog AcNEO found in Adiantum capillus-veneris. The 3D structures of the functional domains were computer-modeled, and the pivotal amino acid sites for each functional domain were also identified. This study represents the first comparative analysis of NEO nucleotide sequences and structures in ferns.