The hydrogen adsorption and desorption processes on the Si(100)(2×1) surface were investigated using in-situ infrared absorption spectroscopy in the multiple internal reflection geometry. It is demonstrated that the distribution of hydride species (SiH, SiH2, and SiH3) significantly changes during adsorption of atomic hydrogen and desorption of molecular hydrogen. At the initial stages of hydrogen adsorption, the monohydride Si (Si–H) and dihydride Si (Si–H2) are populated, with Si–H being dominant. For higher hydrogen exposures the dihydride and trihydride Si are formed. Thermal annealing causes hydrogen to desorb from the hydride species. For annealing temperature up to approximately 400°C, the trihydride Si is etched away, producing a H-terminated surface which consists of monohydride (SiH) and dihydride (SiH2) species. We demonstrate that the conversion from the monohydride to the dihydride phase occurs during thermal annealing.