Understanding electron transport in metal-molecule-metal (MMM) junctions is of great importance for the advancement of molecular electronics. Critical factors that determine conductivity in a MMM junction include the nature of metal-molecule contacts and the electronic structure of the molecular backbone. We have studied the electronic transport property and the valence electronic structure on rigid, conjugated oligoacenes of increasing length with either thiol (-S) or isocyanide (-CN) linkers using conducting probe atomic force microscopy (CP-AFM) and ultraviolet photoelectron spectroscopy (UPS). We find that for these conjugated systems the Au-CN contact is more resistive than Au-S. The difference in contact resistance correlates with UPS measurements that show the highest-occupied molecular orbital (HOMO) of the isocyanide series is lower in energy (relative to the Fermi level of Au) than the HOMO of the thiol series, indicating the presence of a higher tunneling barrier at the contact for the isocyanide-linked molecules. By contrast, the difference in the HOMO positions for the two series of molecules does not appear to affect the length dependence of the junction resistance (i.e., the β value = 0.5 Å-1).