Phycobilisomes (PBSs) are the main accessory light-harvesting complexes in cyanobacteria and their movement between photosystems (PSs) affects cyclic and respiratory electron transport. However, it remains unclear whether the movement of PBSs between PSs also affects the transthylakoid proton gradient (ΔpH). We investigated the effect of PBS movement on ΔpH levels in a unicellular cyanobacterium Synechocystis sp. strain PCC 6803, using glycinebetaine to immobilize and couple PBSs to photosystem II (PSII) or photosystem I (PSI) by applying under far-red or green light, respectively. The immobilization of PBSs at PSII inhibited decreases in ΔpH, as reflected by the slow phase of millisecond-delayed light emission (ms-DLE) that occurs during the movement of PBSs from PSII to PSI. By contrast, the immobilization of PBSs at PSI inhibited the increase in ΔpH that occurs when PBSs move from PSI to PSII. Comparison of the changes in ΔpH and electron transport caused by the movement of PBSs between PSs indicated that the changes in ΔpH were most likely caused by respiratory electron transport. This will further improve our understanding of the physiological role of PBS movement in cyanobacteria. A balanced distribution of the excitation energy absorbed by light-harvesting complexes to the complexes of photosystems I and II (PSI and II) is considered to be one of the most important factors for ensuring optimal photosynthetic efficiency [1][2][3]. In response to fluctuating light conditions, the photosynthetic machinery regulates the distribution of excitation energy between the 2 photosystems (PSs) [4]. This dynamic and rapid process of achieving energy balance is called "state transition" [5,6]. Because phycobilisome (PBS) movement is a prerequisite for cyanobacterial state transitions [7,8], "mobile PBSs" are believed to play a key role in allowing state transitions in cyanobacteria. A recent study indicated that the movement of PBSs between PSII and PSI affects both cyclic and respiratory electron transport [9]. However, it remains unclear whether the movement of *Corresponding author (email: wma@shnu.edu.cn) PBSs between PSs also affects transthylakoid proton gradient (ΔpH) levels in cyanobacterial cells. The aim of this study was to investigate the effect of PBS movement between the 2 PSs on ΔpH levels in cyanobacteria. It is difficult to probe ΔpH levels in vivo as the system relaxes rapidly [10,11]. Millisecond-delayed light emission (ms-DLE) originates from the reverse reaction of the photoact in PSII, and is composed of one fast (within 0.1 s of the onset of measuring flashes) and one slow phase [12,13]. Crofts and his colleagues concluded that the intensities of the fast and slow phases of ms-DLE are stimulated by the membrane potential (ΔE) and the ΔpH, respectively [14][15][16]. Further characteristics and properties of ms-DLE were studied and confirmed in subsequent research [17][18][19][20][21]. It was found that ΔpH levels can be probed in vivo by measuring the slow phase of ms-DLE.