The reductive desorption process of self-assembled monolayers of 1-hexadecanethiol, 1-propanethiol, and 3-mercaptopropionic acid on Au(111) has been studied in 0.5 M KOH solution by in-situ scanning tunneling microscopy (STM) and cyclic voltammetry. In;situ STM images of the monolayers at the potentials between -0.2 V and the reduction potentials of each thiols show the pits that are commonly seen in STM images of thiol self-assembled monolayers. A drastic morphological change takes place in the STM image around the peak potential in a cyclic voltammogram for the reductive desorption of adsorbed thiols. The images indicate that 3-mercaptopropionic acid molecules diffuse away from the surface after the reduction because of its higher solubility, while 1-propanethiol and 1-hexadecanethiol molecules stay in the vicinity of the surface forming aggregates. The partial recovery of the l-hexadecanethiol monolayer after the anodic scan, suggested by cyclic voltammograms, is confirmed by STM, whereas 1-propanethiol aggregates remain at the surface without being reoxidized. The difference in the reoxidation behavior reflects the different amphiphilic properties of the desorbed molecules and the resultant molecular organizations formed on the surface.