In this paper we report the tunneling behavior based on the capillary tunnel junctions of n-octadecylmercaptan (C18H37SH), octadecylamine (C18H37NH2), nonadecanoic acid (C17H35COOH), octadecanol(C18H35COOH), and n-iodooctadecane (C(18)h(37)I), sandwiched between tin and indium electrodes utilizing the naturally existing oxide surfaces, respectively. The surfaces of the electrodes were examined by X-ray diffraction (XRD), atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS) methods, and the self-assembled monolayers adsorbed on the electrode surfaces were inspected by contact angle measurements and XPS. The measured characteristic curves on tin electrode indicated a sequence of energy gaps associated with the specimen: DeltaC(17)H(35)COOH > DeltaC(18)H(37)OH > DeltaC(18)H(37)SH > DeltaC(18)H(37)NH(2) > DeltaC(18)H(37)I. The results on the energy gaps obtained on indium electrodes displayed similar sequence behavior although with different gap values. The experimental observations indicate that the molecule-electrode contact, including both the functional groups and substrates, could contribute jointly to the overall conductance characteristics of molecular junctions.