The evaluation of intramolecular 2H or 13C isotopic composition of vanillin by liquid‐state nuclear magnetic resonance (NMR) is an illustrative example of the analytical challenges associated with molecular authenticity/traceability investigations in food products, and the determination/understanding of metabolic/synthetic pathways. Although isotopic ratio monitoring by 13C NMR (irm‐13C NMR) provides a valuable new source of isotopic information, the analysis of position‐specific (2H/1H) isotopic fractionation of vanillin remains incomplete because of the overlap of two aromatic 2H resonances, and the impossibility of separating these fortuitous isochronous nuclei by isotropic NMR. Exploiting the analytical potential of 2H 2D‐NMR in media containing polypeptide‐based liquid crystals, we show that all aromatic monodeuterated isotopomers can be spectrally discriminated on the basis of 2H residual quadrupolar couplings, ΔνQ(2H), thus enabling the determination of their relative proportions for the first time. After discussing the multiple relevant cofactors leading to the best discrimination and optimization of experimental conditions for reliable quantitative measurements by anisotropic 2D‐NMR, a comparative analysis of six vanillin samples from diverse origins is reported. How the 2H distribution might relate to the biosynthesis of vanillin is discussed.