An unresolved structural issue for [FeFe]-hydrogenases is the nature of the dithiol-bridging ligand in the diiron subcluster of the active site. The two most probable candidates are 1,3-dithiopropane (propane dithiol, PDT) and di-(thiomethyl)-amine (DTN). In the latter case, the dithiol-bridging ligand is assumed to play a major role in the reaction cycle. We report density-functional theory studies of the differing roles of these dithiol-bridging ligands in the infrared spectra of synthetic models and of computational representations of the diiron cluster of the active site. Our analysis shows distinct spectral features associated with the dithiol-bridging NH mode for compounds having a DTN bridge, which, however, would have been obscured by the H2O vibrations in existing measurements. However, if indeed nitrogen is present in the dithiol-bridging ligand, a combination of selective deuteration and chemical inactivation with CO would create a unique signature in an accessible region of the infrared spectrum, whose position and intensity are predicted.