Abstract: In order to evaluate the effects of glyphosate on aquatic organisms in estuary and mudflat, the effects of ammonium glyphone on the superoxidase dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) of Sinonovacula constricta Lamark, Phascolosoma esculenta, and Boleophthalmus pectinirostris were measured using artificial poisoning methods. Furthermore, the effects of glyphone ammonium on the micronuclei in the erythrocyte of B. pectinirostris were also tested using the same method. The results showed that, after exposure under glyphosate of low concentration (63.5 mg/L) for a short period (2 days), the enzyme activities of intestine SOD and CAT and the MDA content of P. esculenta were 231.54, 1.719 U/mg pro. and 0.60 nmol/mg pro., respectively. All the above indexs were significantly or extremely significantly higher than those of the corresponding reference values (204.88, 1.521 U/mg pro. and 0.54 nmol/mg pro.). And with the increase of the treatment concentration of glyphosate, the enzyme activities of SOD and CAT and the MDA content increased. However, 8 days after exposure, the enzyme activities of intestine SOD and CAT and the MDA content of P. esculenta became 155.67, 1.403 U/mg pro. and 0.53 nmol/mg pro., which were significantly lower than those of the control. With the increase of the concentration of glyphosate, the enzyme activities and the MDA content reduced significantly. The effects of glyphosate on the activities of SOD and CAT and the MDA content in the visceral mass of S. constricta and the liver of B. pectinirostris were similar. In addition, the rate of micronuclei and nuclear anomalies in erythrocyte of B. pectinirostris were 17.00‰ and 21.33‰ after 8 days with the treatment of glyphosate in low concentration (53.5 mg/L), which were significantly higher than those of the corresponding control (13.67‰ and 13.33‰). With the increase of the concentration of glyphosate, the ratio of micronuclei and nuclear anomalies in erythrocyte were significantly increased, which demonstrated that B. pectinirostris is sensitive to glyphosate. All results above will contribute to the evaluation of the effects of glyphosate on aquatic organisms in the estuary and mudflat.