We have performed thermoelectric measurements of benzenedithiol (BDT) and C-60 molecules with Ni and Au electrodes using a home-built scanning tunneling microscope. The thermopower of C60 was negative for both Ni and Au electrodes, indicating the transport of carriers through the lowest unoccupied molecular orbital in both cases, as was expected from the work functions. On the other hand, the NiBDTNi junctions exhibited a negative thermopower, whereas the AuBDTAu junctions exhibited a positive thermopower. First-principle calculations revealed that the negative thermopower of NiBDTNi junctions is due to the spin-split hybridized states generated by the highest occupied molecular orbital of BDT coupled with s- and d-states of the Ni electrode.