We observed surprising difference in the FTIR (Fourier transform infrared) hydroxyl spectra of the structurally isomorphous, proton exchanged H-CHA and H-SAPO-34 molecular sieves when measured by transmission (TR) or diffuse reflectance (DRIFT) techniques. Experimental and density functional theory (DFT) based model evidence is presented in this paper to prove that the essential reason for this spectral difference is that DRIFT emphasizes the vibrations of surface hydroxyl sites. Vibrations of the bulk Brønsted acidic hydroxyls shift to higher frequencies when they become surface species, the IR beam is reflected from approximately the top ~15 to 20 Å thick layer of the particles, hence the proportion of surface related IR bands becomes significant compared to the bulk related ones in the DRIFT spectra while the opposite is valid for the TR spectra. We demonstrate that the surface hydroxyls are Brønsted acidic both on the H-CHA and the H-SAPO-34 particles and the upshifted vibrations noticed primarily in the DRIFT spectra are Al-OH vibrations on the surface even of H-SAPO-34, not P-OH groups as most researchers believe. We also show that the bulk Brønsted sites might involve HO1, HO2 and HO4 type hydroxyls associated with the known geometrically different oxygen positions on both molecular sieves, but only HO1 surface hydroxyls are associated with the red-shifted vibration intensified in the DRIFT spectra. Moreover, a single surface model cannot account for every vibration observed in DRIFT spectra. From the combination of IR vibrations of three adequate surface models one can as properly match the experimental DRIFT spectra as the TR spectra from the combination of the calculated bulk HO1…HO4 vibrations of these molsieve crystals.