Reductive desorption processes of a self-assembled monolayer (SAM) of hexanethiol on an Au(111) surface both in H2SO4 and KOH aqueous solutions were investigated by in situ scanning tunneling microscopy (STM) in real time. The structure of the SAM in the electrolyte solutions before the desorption was confirmed to be same as that in the air, that is, the (root3 x root3)R30 degrees structure. The desorption of the thiolate (thiol) molecules was found to be initiated from the defects in the SAM, that is, missing rows and the edge of the vacancy islands. Although the desorbed thiolate (thiol) molecules formed aggregates both in H2SO4 and KOH solutions, the number and the size of the aggregates monitored by STM were higher in H2SO4 solution than in KOH solution, reflecting the lower solubility and diffusion rate of the desorbed molecules in H2SO4 solution than in KOH solution. The reconstructed, that is, (root 3x23), structure of Au(111) was observed after the desorption of the SAM in KOH solution, showing that the clean surface was exposed, although the vacancy islands of monatomic height, which were observed on the SAM-covered gold, remained to be observed on the surface even after the desorption.