We present first-principles based calculation of charge transfer and "band lineup" in molecular electronic devices using as an example the device formed by a phenyldithiolate molecule bridging two gold electrodes and local-spin-density-functional theory with a Gaussian-type orbital basis. We show that significant charge transfer from the metal to the molecule occurs, reflecting the partially ionic character of the sulfur-gold bond and localized in the interfacial region. Such charge transfer increases the electrostatic potential in the molecule which changes the molecular energy level structures. The interaction between the molecular orbitals under the self-consistent potential and the surface metal states determines the lineup of molecular levels relative to the metal Fermi level. We also discuss the implications of our work on device engineering at the molecular scale.