A detailed atomic-resolution scanning tunneling microscopy (STM) and density functional theory study of the adsorption, dissociation, and surface diffusion of phosphine (PH3) on Si(001) is presented. Adsorbate coverages from similar to 0.01 monolayer to saturation are investigated, and adsorption is performed at room temperature and 120 K. It is shown that PH3 dissociates upon adsorption to Si(001) at room temperature to produce both PH2 + H and PH + 2H. These appear in atomic-resolution STM images as features asymmetric-about and centered-upon the dimer rows, respectively. The ratio of PH2 to PH is a function of both dose rate and temperature, and the dissociation of PH2 to PH occurs on a time scale of minutes at room temperature. Time-resolved in situ STM observations of these adsorbates show the surface diffusion of PH2 adsorbates (mediated by its lone pair electrons) and the dissociation of PH2 to PH. The surface diffusion of PH2 results in the formation of hemihydride dimers on low-dosed Si(001) surfaces and the ordering of PH molecules along dimer rows at saturation coverages. The observations presented here have important implications for the fabrication of atomic-scale P dopant structures in Si, and the methodology is applicable to other emerging areas of nanotechnology, such as molecular electronics, where unambiguous molecular identification using STM is necessary.