The mitochondrial inner membrane protease is required for the maturation of mitochondrial proteins that are delivered to the intermembrane space. In the yeast Saccharomyces cerevisiae, this protease is now shown to be a complex that contains two catalytic subunits, Imp2p and the previously identified Imp1p. Primary structure similarity indicates that Imp1p and Imp2p are related to each other and to the family of eubacterial and eukaryotic signal peptidases. Imp1p and Imp2p have separate, nonoverlapping substrate specificities. In addition to its catalyzing the cleavage of intermembrane space sorting signals, Imp2p is required for the stable and functional expression of Imp1p. Thus, inner membrane protease, and by analogy eukaryotic multisubunit signal peptidases, may have acquired multiple catalytic subunits by gene duplication to broaden their range of substrate specificity.