This paper presents the investigation results of the polarized IR spectra of indole-3-carboxaldehyde and 3-acetylindole crystals. Analysis of the results concerned the linear dichroic, H/D isotopic and temperature effects, observed at the frequency ranges of the v N–H and the v N–D bands, respectively. The main spectral properties of the crystals were interpreted in terms of the “strong-coupling” theory on the basis of the hydrogen bond dimeric model. The spectra revealed that the strongest vibrational exciton coupling involved the closely spaced hydrogen bonds, each belonging to a different chain of associated molecules. The paper explains why almost identical shapes of the v N–H and of the v N–D bands characterize these two different crystalline systems. Moreover it is proved that a non-random distribution of protons and deuterons takes place in the lattices of the isotopically diluted crystals. A specific mechanism of the isotopic recognition is the source of this phenomenon.