Theoretical studies suggest that mastering the thermocurrent through single molecules can lead to thermoelectric energy harvesters with unprecedentedly high efficiencies.1–6 This can be achieved by engineering molecule length,7 optimizing the tunnel coupling strength of molecules via chemical anchor groups8 or by creating localized states in the backbone with resulting quantum interference features.4 Empirical verification of these predictions, however, faces considerable experimental challenges and is still awaited. Here we use a novel measurement protocol that simultaneously probes the conductance and thermocurrent flow as a function of bias voltage and gate voltage. We find that the resulting thermocurrent is strongly asymmetric with respect to the gate voltage, with evidence of molecular excited states in the thermocurrent Coulomb diamond maps. These features can be reproduced by a rate-equation model only if it accounts for both the vibrational coupling and the electronic degeneracies, thus giving direct insight into the interplay of electronic and vibrational degrees of freedom, and the role of spin entropy in single molecules. Overall these results show that thermocurrent measurements can be used as a spectroscopic tool to access molecule-specific quantum transport phenomena.