We have studied electrical conduction of conjugated molecules with phenyl rings embedded into alkanethiol self-assembled monolayers (SAMs), to investigate the molecular structural effect on the electrical conduction. Scanning tunneling microscope (STM) images of this surface revealed that the conjugated molecules with phenyl rings adsorbed mainly on defects and domain boundaries of the pre-assembled alkanethiol (nonanethiol C9) SAM and formed conjugated domains. in the case of conjugated molecules with one or three methylene groups between the sulfur and phenyl rings, the measured height of the conjugated molecular domains depended on their lateral sizes, while a strong dependence was not observed in the case of conjugated molecules without a methylene group. By analyzing size dependence on the height of the conjugated molecular domain, we could evaluate the electronic conductivity of the molecular domains. As a result of the analysis, to increase the vertical conduction of the molecular domains, one methylene group was found to be necessary between the sulfur and aromatic phenyl rings. Local barrier heights on the conjugated molecular domains in all the cases were larger than on the C9 SAM surface, suggesting that the increase in the vertical conductivitity is not likely to be due to the lowering of the local barrier height, but can be attributed to the conjugated molecular adsorption. X-ray photoelectron spectra (XPS) and ultraviolet Light photoelectron spectra (UPS) revealed that the carrier density among conjugated molecular SAR;Is does not depend on the number of methylene groups between the sulfur and phenyl rings, suggesting that the higher vertical conduction of conjugated molecules with one methylene group can probably be attributed to higher transfer probability of carriers during the STM measurements.