Crystalline and amorphous transition metal chalcogenides such as MoS2 are currently recognized as state-of-the-art non-precious transition metal catalysts for the hydrogen evolution reaction (HER). Nevertheless, despite numerous studies dedicated to their electrocatalytic activities, the exact nature of the active sites as well as their interaction with interfacial water remain largely elusive. In this work, amorphous and crystalline MoS2 catalysts were prepared by electrodeposition and chemical exfoliation respectively, and compared with other Mo-based compounds. Herein, we show that all those compounds exhibit two reduction mechanisms in low proton concentration: the proton reduction occurring at low overpotential followed by the water reduction at higher overpotential. We show that both the chemical composition and the structure of the catalyst influence the activity of the proton reduction, but that none of those materials efficiently catalyzes the water reduction. Finally, we could demonstrate by using different cations (Li+, Na+ and K+) or using deuterated electrolytes that the active sites for the proton reduction mechanism is probably different for amorphous and exfoliated crystalline MoS2.