In this series on the application of configuration analysis (CA) to the electronic excited states of photobiological receptors, we have extended CA to two important photobiological receptors, phytochrome of photomorphogenic and biological clock systems and stentorin of the photophobic response system of stentors. In addition, the effect of substituents in chlorophylls on the electronic excitation of the chlorin and bacteriochlorin ring systems has been examined. The open-shell calculations of chlorophylls have also been performed.In the singlet excited state of phytochrome, there is a significant charge transfer from ring A to the violin moiety of the phytochrome molecule, with a tendency for the localized excitation in the A ring. The charge transfer contribution to the singlet-singlet excitation is also significant. These results are correlated with the photomorphogenic transformation of phytochrome which involves deprotonation and/or tautomerism of the ring A in the excited state. In the case of stentorin, the excitation resides largely in the aromatic system, with some charge transfer to the carbonyl groups. The photobiological significance of these results are discussed.