The electronic absorption spectrum of the homodimeric special pair in bacterial photosynthetic reaction centers is greatly modified when one of the bacteriochlorophylls is replaced by a bacteriopheophytin to form a heterodimer. The absorption exhibits further unusual changes when hydrogen bonds from the protein to conjugated carbonyl groups are added or removed. In order to explain these absorption features, we postulate a charge resonance interaction between the lowest energy exciton state of the special pair and an intradimer charge transfer state. A general theory is developed that is closely related to the formalism of Fano’s treatment for atomic absorption line shapes associated with autoionization (Fano, U. Phys. Rev 1961 124, 1866). Three different charge resonance limits are discussed, which depend on the relative magnitudes of the electronic coupling between the exciton state and charge transfer state and the vibronic bandwidth of the charge transfer state. In the intermediate charge resonance limit, two broad bands are predicted, and this corresponds closely to the unusual absorption line shape observed for the heterodimer. Furthermore, the systematic variations in the absorption line shapes for four different heterodimer/hydrogen bond mutants can be satisfactorily explained by shifting the relative energies of the exciton and charge transfer states. This leads to the conclusion that the BChl(+)BPhe(-) intraheterodimer charge transfer state is primarily responsible for the charge resonance interaction, providing information on the absolute energy of this functionally-relevant state and the electronic coupling. This treatment is generally applicable to absorption line shapes in related systems and can be used to provide a unified treatment of the absorption spectra of a large variety of available perturbed homo- and heterodimers.