Prolyl endopeptidase and dipeptidyl peptidase IV are serine proteases which cleave the peptide bonds at the carboxy group of proline residues. They do not show amino acid sequence homology with the known serine enzymes, but a possible relationship between them has not yet been examined. We have compared the amino acid sequences, and this revealed a distant evolutionary relationship between the two enzymes. Conserved segments were found mainly in the C-terminal region which also contained the catalytic residues. It is concluded that the C-terminal region is a protease domain which is attached to some noncatalytic structures.