Amorphous molybdenum sulfide (MoS x ) is currently being developed as an economically viable and efficient catalyst for the electrochemical hydrogen evolution reaction (HER). An important yet unsolved problem in this ongoing effort is the identification of its catalytically active sites for proton reduction. In this work, cyclic voltammetry (CV), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy were used to investigate the catalytically active sites and structural evolution of MoS x films during HER in 1 M HClO4 electrolyte. Transformation of anodically deposited MoS x (x ≈ 3) to a structure with MoS2 composition during the cathodic sweep of a CV was demonstrated using XPS and operando Raman spectroscopy. Interestingly, a Raman peak at 2530 cm–1 was recorded at potentials relevant to H2 evolution, which we ascribed to the S–H stretching vibration of MoS x –H moieties. This assignment was corroborated by H/D isotope exchange experiments. Mo–H (or Mo–D) stretching vibrations were not observed, which thus allowed us to rule out Mo centers as catalytic sites for proton reduction to H2. Density functional theory (DFT) calculations were performed on a variety of MoS x structures to capture the heterogeneous nature of amorphous materials and corroborated the assignments of the observed vibrational frequencies. On the basis of these experimental measurements and quantum chemical simulations, we have for the first time directly pinpointed the sulfur atoms in amorphous MoS x to be the catalytically active sites for evolving H2.