We re-visit the phenomenon of persistent spectral hole-burning (PSHB) in isolated PS II reaction centers in light of advances in the understanding of the overall electronic structure of PS II. A recent analysis of non-selective photochemical hole-burning and the consequent changes in CD spectra associated with the photo-reduction of Pheo D1 (the primary electron acceptor) supports an analysis in which very substantial and non-correlated chlorin site-energy inhomogeneity leads to a range of realizations of the exciton structure of reaction centers. The lowest energy excited state can be described as predominantly involving the dominantly Chl D1 (the primary acceptor) exciton, but in a significant fraction of centers the lowest excited state is a dominantly Pheo D2 (the inactive pheophytin) exciton. The narrow linewidth of PSHB reported a decade ago in these systems, with homogeneous holewidths approaching that corresponding to the radiative lifetime, along with our ability to reproduce the published PSHB action spectrum, leads to the suggestion that aspects of hole-burning in these systems can be attributed to centers in which the exciton realizations lead to a predominantly Pheo D2 character as the lowest energy exciton. This assignment is discussed in terms of models of the PS II reaction center.