Recent studies on the upgrade of cellulosic biomass to renewable chemicals and fuels based on Ru/ZrO2 catalysts have shown that the catalyst contains atomically dispersed, highly stable Ru atoms. FTIR spectra after CO dosage reveal a complex manifold of bands resulting from Ru‐CO carbonyl species. The nature of the atomically dispersed Ru species on monoclinic zirconia, and the origin of their thermal stability are the object of this investigation. Combining density functional theory (DFT) calculations on model systems of both tetragonal and monoclinic ZrO2, with novel experimental data, we provide a basis for the identification of the monoatomic Ru species. Various candidates are explored based on DFT calculations of their intrinsic stability and of the vibrational properties of adsorbed CO probe molecules. The results allow us to discard a number of possible structures, and restrict the analysis to a few potential candidates. Most likely, the atomically dispersed sites result from the interaction of Ru atoms with one OH group of the surface with elimination of H2 by condensation, leaving RuO species strongly bound to the zirconia surface. CO binds strongly to the RuO units forming (RuO)(CO)2 geminal complexes with characteristic signatures in terms of CO vibrational frequency. Despite the formal positive oxidation state of the Ru species, large negative shifts are found in the CO stretching frequency compared with the free CO molecule.