This paper deals with the comparative studies of SAMs formed in ethanolic solution of alkanethiol as well as from neat alkanethiol. We have characterized the SAMs using electrochemical techniques like Cyclic Voltammetry and Electrochemical Impedance Spectroscopy as well as by non- electrochemical techniques like Scanning Tunneling Microscopy (STM) and Grazing Angle FT-IR Spectroscopy. Our experimental results prove that neat alkanethiot SAMs are more ordered and impermeable and exhibits excellent barrier properties in aqueous medium compared to the monolayer formed in ethanol. The lower permeability and better barrier property of neat alkanethiol SAM has been shown to be due to the formation of larger hydrophobic domains compared to I mM HDT coated surface. This was confirmed by our STM studies on the alkanethiol coated Au surface.