Peridinin-chlorophyll-protein (PCP) complexes, where the N-terminal domain of native PCP from Amphidinium carterae has been reconstituted with different chlorophyll (Chl) species, have been investigated by time-resolved EPR in order to elucidate the details of the triplet-triplet energy transfer (TTET) mechanism. This spectroscopic approach exploits the concept of spin conservation during TTET, which leads to recognizable spin-polarization effects in the observed time-resolved EPR spectra. The spin polarization produced at the acceptor site (peridinin) depends on the initial polarization of the donor (chlorophyll) and on the relative geometric arrangement of the donor-acceptor spin axes. A variation of the donor triplet state properties in terms of population probabilities or triplet spin axis directions, as produced by replacement of chlorophyll a (Chl a) with non-native chlorophyll species (ZnChl a and BacterioChl a) in the reconstituted complexes, is unambiguously reflected in the polarization pattern of the carotenoid triplet state. For the first time, in the present investigation spin-polarization conservation has been shown to occur among natural cofactors in protein complexes during the TTET process. Proving the validity of the assumption of spin conservation adopted in the EPR spectral analysis, the results reinforce the hypothesis that in PCP proteins peridinin 614, according to X-ray nomenclature (Hofmann, E.; et al. Science 1996, 272, 1788-1791), is the carotenoid of election in the photoprotection mechanism based on TTET.