Using first order perturbation theory, we show that the bandwidth, intensity, and lineshape in transmission spectra of a single molecular junction calculated by the non-equilibrium Green's function (NEGF) method can be rationalized by the one- and two-resonant state approximations. Particularly, we find that the lineshape of the transmission function is strongly influenced by the relative phases between the two nearest-neighbor resonant states. Finally, we utilize these results to examine two systems: a Huckel model system with five sites and a single fluoro-1,4-benzenedithiol molecule within the extended Huckel approximation. (C) 2008 Published by Elsevier B.V.