By trapping molecules between two gold electrodes with a temperature difference across them, the junction Seebeck coefficients of 1,4-benzenedithiol (BDT), 4,4′-dibenzenedithiol, and 4,4′′-tribenzenedithiol in contact with gold were measured at room temperature to be +8.7 ± 2.1 microvolts per kelvin (μV/K), +12.9 ± 2.2 μV/K, and +14.2 ± 3.2 μV/K, respectively (where the error is the full width half maximum of the statistical distributions). The positive sign unambiguously indicates p-type (hole) conduction in these heterojunctions, whereas the Au Fermi level position for Au-BDT-Au junctions was identified to be 1.2 eV above the highest occupied molecular orbital level of BDT. The ability to study thermoelectricity in molecular junctions provides the opportunity to address these fundamental unanswered questions about their electronic structure and to begin exploring molecular thermoelectric energy conversion.