The tunneling resistance and electronic structure of metal-molecule-metal junctions based on oligoacene (benzene, naphthalene, anthracene, and tetracene) thiol and dithiol molecules were measured and correlated using conducting probe atomic force microscopy (CP-AFM) in conjunction with ultraviolet photoelectron spectroscopy (UPS). Nanoscopic tunnel junctions (∼10 nm2) were formed by contacting oligoacene self-assembled monolayers (SAMs) on flat Ag, Au, or Pt substrates with metalized AFM tips (Ag, Au, or Pt). The low bias (<0.2 V) junction resistance (R) increased exponentially with molecular length (s), i.e., R = R0 exp(βs), where R0 is the contact resistance and β is the tunneling attenuation factor. The R0 values for oligoacene dithiols were 2 orders of magnitude less than those of oligoacene thiols. Likewise, the β value was 0.5 per ring (0.2 Å-1) for the dithiol series and 1.0 per ring (0.5 Å-1) for the monothiol series, demonstrating that β is not simply a characteristic of the molecular backbone but is strongly affected by the number of chemical (metal-S) contacts. R0 decreased strongly as the contact work function (Φ) increased for both monothiol and dithiol junctions, whereas β was independent of Φ within error. This divergent behavior was explained in terms of the metal-S bond dipoles and the electronic structure of the junction; namely, β is independent of contact type because of weak Fermi level pinning (UPS revealed EF - EHOMO varied only weakly with Φ), but R0 varies strongly with contact type because of the strong metal-S bond dipoles that are responsible for the Fermi level pinning. A previously published triple barrier model for molecular junctions was invoked to rationalize these results in which R0 is determined by the contact barriers, which are proportional to the size of the interfacial bond dipoles, and β is determined by the bridge barrier, E F - EHOMO. Current-voltage (I-V) characteristics obtained over a larger voltage range 0-1 V revealed a characteristic transition voltage Vtrans at which the current increased more sharply with voltage. Vtrans values were generally >0.5 V and were well correlated with the bridge barrier EF - EHOMO. Overall, the combination of electronic structure determination by UPS with length- and work function-dependent transport measurements provides a remarkably comprehensive picture of tunneling transport in molecular junctions based on oligoacenes.