A cDNA encoding preprocathepsin C was isolated from adults of the asian blood fluke Schistosoma japonicum. The deduced amino acid sequence of S. japonicum cathepsin C comprised 458 amino acid residues; 22 NH2-terminal residues corresponding to the signal peptide, 199 residues corresponding to the propeptide and 237 COOH-terminal residues corresponding to the mature enzyme region. The amino acid sequence of this preprocathepsin showed 43% and 50% identity to that of human and rat, respectively. The preproenzyme shared only 59% identity with the sequence for a cathepsin C reported from Schistosoma mansoni, differing from it in active-site residues and in its potential N-glycosylation sites. Northern-blot analysis showed that S. japonicum cathepsin C was expressed in greater quantities in female than in male parasites. Phylogenetic analysis utilizing the mature enzyme sequences of S. japonicum and other cathepsin Cs demonstrated that cathepsin Cs and cathepsin Bs shared a common ancestry. The unusually long prosegment observed in cathepsin C from S. japonicum and from other species was compared to that of cathepsin Bs and cathepsin Ls. The extension contained two blocks of residues which were highly conserved among cathepsin Cs. The COOH terminus of the prosegment exhibited a composite of features present in the prosegments of cathepsin Ls and cathepsin Bs. Most significantly, given the common ancestry of cathepsin B and cathepsin C, the prosegment of cathepsin C included ERFNIN-like motifs and other residues more characteristic of non-cathepsin-B-like members of the papain superfamily such as cathepsin L.