Using a novel, pulsed micro-second time-resolved photoacoustic (PA) instrument, we measured thermal dissipation and energy storage (ES) in the intact cells of wild type (WT) Chlamydomonas reinhardtii, and mutants lacking either PSI or PSII reaction centers (RCs). On this time scale, the kinetic contributions of the thermal expansion component due to heat dissipation of absorbed energy and the negative volume change due to electrostriction induced by charge separation in each of the photosystems could be readily distinguished. Kinetic analysis revealed that PSI and PSII RCs exhibit strikingly different PA signals where PSI is characterized by a strong electrostriction signal and a weak thermal expansion component while PSII has a small electrostriction component and large thermal expansion. The calculated ES efficiencies at ~10 μs were estimated to be 80 ± 5 and 50 ± 13% for PSII-deficient mutants and PSI-deficient mutants, respectively, and 67 ± 2% for WT. The overall ES efficiency was positively correlated with the ratio of PSI to PSI + PSII. Our results suggest that the shallow excitonic trap in PSII limits the efficiency of ES as a result of an evolutionary frozen metabolic framework of two photosystems in all oxygenic photoautotrophs.