A new full-length genomic DNA, encoding a member of the cyanovirin-N (CV-N) homologous protein family, has been cloned from the fern species Ceratopteris thalictroides by chromosome walking. It is 1993 bp long, contains a 723 bp open reading frame (ORF) that encodes a deduced protein (named CtCVNH) with 150 amino acid residues. CtCVNH has a predicted isoelectric point (PI) of 4.47 and a calculated molecular mass 15.9556 kDa. It possesses the conserved anti-HIV (human immunodeficiency virus) CV-N domain, which is the same as the cyanovirin-N homology (CVNH) members that were isolated from filamentous ascomycetes and C. richardii. Modeling of the tertiary structure indicated that CtCVNH is an elongated, largely β-sheet protein that displays internal two-fold pseudosymmetry. Comparative structure analysis of the predicted CtCVNH with native CV-N revealed that the major evolutionary changes occurring during the evolution of plant CVNHs were: 1) a length increase at N- and C-terminal regions; and 2) a loop to helix transition at the helical-turn regions. Phylogenetic analysis showed that CtCVNH was grouped together with the two CVNHs from C. richardii.