Isolated reaction centers (RCs) from wild-type Chlamydomonas (C.) reinhardtii of Photosystem II (PSII), at different levels of intactness, were studied to provide more insight into the nature of the charge-separation (CS) pathway(s). We argue that previously studied DI/D2/Cyt(b559) complexes (referred to as RC680), with Chip, serving as the primary electron donor, contain destabilized D1 and D2 polypeptides and, as a result, do not provide a representative model system for the intact RC within the PSII core. The shapes of nonresonant transient hole-burned (HB) spectra obtained for more intact RCs (referred to as RC684) are very similar to P(+)Q(A)(-) - PQ(A) absorbance difference and triplet minus singlet spectra measured in PSII core complexes from Synechocystis PCC 6803 [Schlodder et al. Philos. Trans. R. Soc. London, Ser. B 2008, 363, 1197]. We show that in the RC684 complexes, both P-D1 and Chl(D1) may serve as primary electron donors, leading to two different charge separation pathways. Resonant FIB spectra cannot distinguish the CS times corresponding to different paths, but it is likely that the zero-phonon holes (ZPHs) observed in the 680-685 nm region (corresponding to CS times of similar to 4.4-4.4 ps) reveal the Chl(D1) pathway; conversely, the observation of charge-transfer (CT) state(s) in RC684 (in the 686-695 nm range) and the absence of ZPHs at lambda(B) > 685 nm likely stem from the P-D1 pathway, for which CS could be faster than I ps. This is consistent with the finding of Krausz et al. [Photochem. Photobiol. Sci. 2005, 4, 744] that CS in intact PSII core complexes can be initiated at low temperatures with fairly long-wavelength excitation. The lack of a clear shift of HB spectra as a function of excitation wavelength within the red-tail of the absorption (i.e., 686-695 nm) and the absence of ZPHs suggest that the lowest-energy CT state is largely homogeneously broadened. On the other hand, in usually studied destabilized RCs, that is, RC680, for which CT states have never been experimentally observed, Chip, is the most likely electron donor.