Abstract: In this study, we investigated the effects of N-phenyl-2-naphthylamine, a type of allelochemical, on the invasive cyanobacteria Cylindrospermopsis raciborskii. We measured the growth, the activities of antioxidative enzymes, and polyphasic Chl. a fluorescence transients of Cylindrospermopsis raciborskii that was cultured in the presence of N-phenyl-2-naphthylamine at different concentrations (0, 0.05, 0.10, 0.50, 1.00 and 2.00 mg/L). When the concentration of N-phenyl-2-naphthylamine was higher than 0.50 mg/L, the Chl. a content was significantly lower than the control. This indicated that the level of Chl. a could be reduced by the increase in N-phenyl-2-naphthylamine. The EC50 of N-phenyl-2-naphthylamine on C. raciborskii was 1.02 mg/L after a 72h exposure. At the concentration lower than 0.50 mg/L, N-phenyl-2-naphthylamine caused a significant increase in a variety of parameters of polyphasic Chl. a fluorescence transients, including the maximum quantum yield of primary photochemistry (Po), the density of RCs(RC/CSo), the performance index on absorption basis (PIABS), and the performance index on cross section basis (PICS). One exception was o that declined in the presence of low concentration of N-phenyl-2-naphthylamine. On the other hand, Po, RC/CSo, PIABS, PICS, and o were all reduced when the concentration of N-phenyl-2-naphthylamine was higher than 0.50 mg/L (eg. 1.00 mg/L and 2.00 mg/L). These data suggested that low dose of N-phenyl-2-naphthylamine might promote the photosynthetic efficiency of C. raciborskii, while high dose could reduce density of RCs and harm the PSⅡ and electron transfer, and thus result in the inhibition of photosynthetic efficiency in C. raciborskii. Compared to the control, the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) were all obviously elevated along with the increase in N-phenyl-2-naphthylamine concentration. This implied that C. raciborskii might counter the damage of N-phenyl-2-naphthylamine with enhanced antioxidant enzymatic activities. In conclusion, N-phenyl-2-naphthylamine could inhibit the growth of C. raciborskii by disrupting the electron transfer of PSⅡ and lowering the density of RCs, and therefore it could be considered as a potential compound for the control of Cylindrospermopsis blooming.