We use femtosecond transient absorption spectroscopy to study chlorophyll (Chl)-Chl energy transfer in the peridinin-chlorophyll protein (PCP) reconstituted with mixtures of either chlorophyll b (Chlb) and Chld or Chla and bacteriochlorophyll a (BChla). Analysis of absorption and transient absorption spectra demonstrated that reconstitution with chlorophyll mixtures produces a significant fraction of PCP complexes that contains a different Chl in each domain of the PCP monomer. The data also suggest that binding affinity of Chla is less than that of the other three Chl species. By exciting the Chl species lying at higher energy, we obtained energy transfer times of 40 ± 5 ps (Chlb-Chld) and 59 ± 3 ps (Chla-BChla). The experimental values match those obtained from the Förster equation, 36 and 50 ps, respectively, showing that energy transfer proceeds via the Förster mechanism. Excitation of peridinin in the PCP complex reconstituted with Chla/BChla mixture provided time constants of 2.6 and 0.4 ps for the peridinin-Chla and peridinin-BChla energy transfer, matching those obtained from studies of PCP complexes reconstituted with single chlorophyll species.