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Manganese (Mn) excess is a major abiotic stress for plant growth. In the present study, we investigated the effects of Mn on photosynthesis in Ligustrum lucidum and Melia azedarach leaves using chlorophyll fluorescence transients. Both plant species were exposed to two Mn concentrations (0.5 and 1 mmol) for 10 and 30 d. Results showed that excess Mn significantly inhibited photosynthesis. With the increase of Mn concentration and stress time, the inhibition was more serious. Mn stress impaired PSII at the donor and the acceptor side by damaging the oxygen-evolving complex and limiting electron transport downstream of QA in both trees. A significant decline in 820 nm reflection curve absorption was observed in M. azedarach, suggesting that the oxidization-reduction reactions in PSI were inhibited but this phenomenon was not observed in L. lucidum. Therefore, excess Mn impaired the whole electron transport chain associated with inactive PSII reaction centers in Ligustrum lucidum and inhibited oxidization-reduction reactions in PSI in M. azedarach.