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Seagrasses play an important role in coastal marine ecosystems, but they have been increasingly threatened by human activities. In recent years, seagrass communities have rapidly degenerated in the coastal marine ecosystems of China. To identify the reasons for the decline in seagrasses, the phytotoxic effects of trace metals (Cu, Cd and Zn) on the seagrass Thalassia hemprichii were investigated, and the environmental contents of the metals were analyzed where the seagrass grows. The results showed that leaf necrosis in T. hemprichii exposed to 0.01-0.1 mg L−1 of Cu2+ for 5 days was more serious than that in plants exposed to the same concentrations of Cd2+ and Zn2+. The chlorophyll content in T. hemprichii declined in a concentration-dependent manner after 5 days of exposure to Cu2+, Cd2+ and Zn2+. The evident reduction in ΔF/Fm’ in T. hemprichii leaves was observed at day 1 of exposure to 0.01-1.0 mg L−1 of Cu2+ and at day 3 of exposure to 0.1-1.0 mg L−1 of Cd2+. The antioxidant enzyme activities (SOD, POD and CAT) in T. hemprichii leaves exposed to the three metal ions also showed significant changes. In seawater from Xincun Bay (Hainan, China), where T. hemprichii grows, Cu had reached a concentration (i.e., 0.01 mg L−1) that could significantly reduce chlorophyll content and ΔF/Fm’ in T. hemprichii leaves. Our results indicate that Cu influences the deterioration of seagrasses in Xincun Bay. [ABSTRACT FROM AUTHOR]