Fluorescence spectra of native purple bacterial reaction center (RC) and bacterial pheophytin (Bphe) replaced RCs were obtained from 600 nm to 900 nm with a selective excitation at 597 nm. With the help of measuring the fluorescence from bacterial chlorophyll, bacterial pheophytin and plant pheophytin, the corresponding components in the RCs are classified for fluorescence emission. Results showed that pheophytin substitution influences the composition of fluorescence spectra. Therefore, four, three and two components were obtained from fluorescence spectra of native RC, Bphe B_replaced RC and Bphe A,B _replaced RC, respectively. Fluorescence components are well correlated to the binding of plant pheophytin. The decay of excited state of primary electron donor P in different RCs was also studied by measuring the fluorescence decay at 686.4, 674.1 and 681.1 nm, respectively. The decaying kinetics changed in different RCs, indicating that pheophytin replacement influenced the energy transduction and primary photochemical reaction in purple bacterial reaction centers.