Transition metal oxide overlayers are an important class of heterogeneous catalysts (sometimes referred to as monolayer catalysts), both for model studies and numerous industrial processes. To determine the molecular structures in such amorphous thin layers requires application of characterization methods that can perform in the absence of long-range order and can distinguish between different molecular structures of the same metal oxide (e.g., isolated VO4, isolated VO5, isolated VO6, dimeric V2O7, oligomeric (VO3)n, etc.). Vibrational spectroscopy (IR and Raman) is the method of choice for this purpose since it can discriminate among multiple molecular structures and can function at high temperatures and pressures in presence of reactive gas phases (oxidizing, reducing and in between). Thus, IR and Raman spectroscopy uniquely provide access to in situ and operando molecular spectroscopy studies under relevant catalytic reaction conditions. In the present review, a comprehensive overview of the various possibilities to structurally and chemically characterize oxide overlayers with vibrational spectroscopy is presented and the progress achieved so far in this field is summarized. The surface molecular structures of supported transition metal oxide layers on oxide supports are described in detail, focusing in particular on those vibrational modes that can be used for precise molecular structural determination. The structural response of such surface oxide species to environmental conditions (ambient, dehydrated, reduced, reaction conditions) is reviewed. The approaches employed to characterize adsorption and reaction sites by the adsorption of suitable probe molecules or by performing in situ or operando studies will be discussed in detail. Additionally, the use of vibrational spectroscopy to study more complex systems will be highlighted, such as the formation of native oxide overlayers on complex oxides or even metal particles (e.g., during strong metal–support interactions).