Abstract: The wide distribution of antibiotics in various environmental media may pose a threat to aquatic ecosystem and non-target organisms. Florfenicol (FFC) is one of the most common used antibiotics in aquaculture. Its sustained release and degradation-resistance lead to the phenomenon of “pseudo-persistent” in aquatic environment. Microalgae are the primary producer in aquatic ecosystems, rich in polysaccharides, polyunsaturated fatty acids and carotenoids, and are also an important bait for marine bivalve larva. To explore the effects of antibiotic residues in aquatic environment, FFC (0.001, 0.01, 0.1, 1.0, 10, 20 and 50 mg/L) were treated the marine microalgae Isochrysis galbana for 72h, and algal growth, photosynthetic pigments contents and fatty acids were determined. The results showed that FFC at low concentrations (<1 mg/L) promoted the algal growth, and it had opposite effect at 10—50 mg/L. The half maximal effective concentration (EC₅₀) of FFC on I. galbana at 72h was 17.12 mg/L and the toxicity of this EC₅₀ belonged to moderate. The intracellular FFC concentration was elevated with the increased dose, reaching a maximum of 122 μg/mL in 50 mg/L treatment group. FFC (>1 mg/L) significantly decreased the contents of fatty acids and chlorophyⅡ, while significantly increased the content of carotenoids. In summary, low concentrations of antibiotics in aquatic environment may incur phytoplankton and red tide outbreaks. Changes in chlorophyⅡ content indicated that FFC may interfere the normal photosynthetic process and chlorophyⅡ synthesis of I. galbana. Carotenoids are critical photoprotective pigments, which absorb extra energy in chloroplast and avoid the damage of cell membrane from reactive oxygen species. Under the stress of FFC exposure (>1 mg/L) the induced carotenoids content and reduced fatty acids of I. galbana had protective role. The present study highlighted the potential risk of antibiotic residues in aquatic environment on algae, which provided theoretical support for the rational use of antibiotics in aquaculture.