Controlling the intrinsic optical and electronic properties of a single molecule adsorbed on a surface requires electronic decoupling of some molecular orbitals from the surface states. Scanning tunneling microscopy experiments and density functional theory calculations are used to study a perylene molecule derivative (DHH-PTCDI), adsorbed on the clean 3 × 3 reconstructed wide band gap silicon carbide surface (SiC(0001)-3 × 3). We find that the LUMO of the adsorbed molecule is invisible in I(V) spectra due to the absence of any surface or bulk states and that the HOMO has a very low saturation current in I(z) spectra. These results present a paradox that the molecular orbitals are electronically isolated from the surface of the wide band gap semiconductor even though strong chemical bonds are formed.