We present a combined experimental and theoretical study of molecular methanethiol ͑CH 3 SH͒ adsorption on the reconstructed Au͑111͒ surface in the temperature range between 90 and 300 K in UHV. We find that the simplest thiol molecules form two stable self-assembled monolayer ͑SAM͒ structures that are created by distinct processes. Below 120 K, a solid rectangular phase, preserving the herringbone reconstruction, emerges from individual chains of spontaneously formed dimers. At higher adsorption temperatures below 170 K, a close-packed phase forms via dissociative CH 3 SH adsorption and the formation of Au adatoms that are not incorporated into the SAM. We show that the combination of a strong substrate-mediated interaction with nondissociative dimerization and temperature activated removal of the Au͑111͒ reconstruction drives the largescale assembly of molecular CH 3 SH into two distinct phases.