We present a detailed analysis of Raman and infrared (IR) phonon spectra of strongly luminescent nonstoichiometric M−In−S (M = Cu, Ag, Hg) and core/shell M−In-S/ZnS nanocrystals (NCs) of small size (d ≈ 2−4 nm), formed by means of aqueous colloidal chemistry under mild conditions. Despite presumably similar factors determining position and broadening of the Raman and X-ray diffraction (XRD) peaks, phonon spectra are shown to be more sensitive to NC composition and crystals structure. The spectral Raman pattern of these strongly Mdeficient M−In-S NCs is different from that of the corresponding stoichiometric phases, e.g., CuInS 2 or AgIn 5 S 8 , and excludes its assignment to relevant binary sulfides, e.g., In 2 S 3 . Resonant behavior of relative peak intensities in Raman spectra is different from that of larger-size stoichiometric NCs and bulk samples studied before, while the temperature dependence reveals an analogous enhancement of the highest-frequency LO modes supporting an unambiguous assignment of the latter. Therefore, we conclude that the Raman spectra observed are characteristic of the specific structure of these highly nonstoichiometric small NCs. IR modes of these NCs occur in the same frequency range as the Raman ones but at higher frequencies than the IR phonons in bulk material. The IR spectra are less characteristic, compared to Raman ones, revealing more similarity among the three NC compounds and with the bulk counterparts.