Abstract: Large-scale cultivation of eucalyptus has been seen along the coastal zone in Southern China in recent years. A number of studies have investigated the effect of eucalyptus allelopathic on land plants. However, little information is available about the impact of eucalyptus on marine primary productivity as well as the whole marine ecosystem. In the present study, we used the chlorophyll fluorescence technology (Water-PAM) to examine the changes of the chlorophyll fluorescence parameters (F_v/F_0, F_v/F_m, Yield and ETR) of Dicrateria zhanjiangensis and Chaetoceros gracilis, when they were exposed to aqueous extract of eucalyptus leaves. Meanwhile, the growth of two species of marine microalgae was observed during the exposure. The results showed that the low concentrations (e.g., 0.4,0.8,1.2mL/L) of the aqueous extract of eucalyptus leaves have little effect (P>0.05) on four chlorophyll fluorescence parameters of Dicrateria zhanjiangensis within 96h. High concentration (2.0mL/L) of the aqueous extract of eucalyptus leaves, however, could significantly affected the four chlorophyll fluorescence parameters of Dicrateria zhanjiangensis, which all reached the lowest values at 24h post-exposure and the second lowest at 48h post-exposure. Nevertheless, when the samples were treated with a high concentration of 2.0mL/L maintained for 72and 96h, the inbibitory effect of extract on chlorophyll fluorescence parameters disappeared. Apparently, higher concentrations (≥2.0mL/L) of the aqueous extract of eucalyptus leaves have an inhibitory effect on chlorophyll fluorescence parameters in the early stage of exposure (within 48h). For Chaetoceros gracilis, when it was exposed to low concentrations of 0.4and 0.8mL/L of the aqueous extract of eucalyptus leaves for 24and 48h, its four chlorophyll fluorescence parameters increased with concentrations used. However, when it was exposed to high concentration (2.0mL/L) of the aqueous extract of eucalyptus leaves, F_v/F_m of Chaetoceros gracilis reduced to the minimum at 24h post-exposure, whereas, the other three fluorescence parameters remained in the normal range. In the late stage of exposure (72and 96h), four chlorophyll fluorescence parameters of Chaetoceros gracilis increased with the concentrations. In addition, the aqueous extract of eucalyptus leaves has a significant inhibitory effect on growth of both two species of microalgae, as evidenced by the observation of a dose dependent inhibition of growth by aqueous extract. In conclusion, the study showed that the aqueous extract of eucalyptus leaves has significant effects on either growth or chlorophyll function of two species of marine microalgae. And thus, eucalyptus should have profound impact on the whole marine ecosystem.