The thermophilic phototroph Chloroflexus aurantiacus possesses a photosynthetic reaction center (RC) containing a pair of menaquinones acting as primary (MQA) and secondary (MQB) electron acceptors and a tetraheme cytochrome c554 as an electron donor. We used native, chlorosome-containing photosynthetic membranes of this bacterium to study the MQB turnover. The binary oscillations of the semiquinone form MQB- in response to a train of short light flashes were monitored at 416 nm, in the isosbestic point of the light-induced difference spectrum of cytochrome c554. After the first flash MQB- was formed, after the second one it disappeared due to the MQA-MQB- → MQAMQBH2 transition. The latter reaction was kinetically resolved by means of electrometry. For this purpose chromatophores of Chl. aurantiacus were adsorbed onto a phospholipid and menaquinone-impregnated collodion film. We found that after the second excitation flash, but not after the first one, the photoelectric response included, in addition to the fast kinetic components reflecting the charge separation between the tetraheme cytochrome c and MQA, a slower kinetic component with a rise time of 3 µs (pH = 8.3) and a relative amplitude of about 10% of the charge separation phase in the RC. We attributed this reaction to the electrogenic proton transfer which accompanied the transfer of the second electron during the MQA-MQB- → MQAMQBH2 transition. The rise time of the same reaction was reported to be almost three orders of magnitude slower in the isolated, proteoliposome-incorporated RC from this bacterium. The possible reasons of the faster turnover rates observed in the chlorosome-carrying native membrane preparations from Chl. aurantiacus are discussed.