Cyclooxygenase (COX) is crucial in inflammation and plays important role in cerebral ischemia. Antiinflammatory effects of melatonin have been verified in previous studies. In this study, cerebral blood flow (CBF) was monitored during operation, infarct volume (IFV) was determined with 5-triphenyltetrazolium chloride (TTC) staining and MR image, and neurological functions were evaluated with turn in an alley and fall pole test in both COX1-gene knockout and wide-type mice with or without melatonin administration 3 days after photothrombosis. CBF reduction, IFV and neurological deficits were not significantly different in COX-1 wild-type and COX-1 knockout mice. Melatonin (15 mg/kg) intraperitoneal injection decreased the CBF reduction, IFV and the latency to turn in an alley in COX-1 wide-type mice, whereas the neuroprotective effect of melatonin was attenuated in COX-1 knockout mice. We concluded that melatonin reduced susceptibility to photothrombotic stroke. COX-1 gene knockout does not alter the susceptibility to cerebral ischemia caused by photothrombosis. COX-1 plays an important role in the pathway of the protection of melatonin.