This study was performed to investigate the application of bovine amniotic membrane for canine corneal ulcer and to compare bovine amniotic membrane flap to nictitating membrane flap. Corneas were treated with 8.0mm trephine and 100% ethanol was applied and corneal epithelium was removed. This experiment was divided into three groups; control group, nictitating membrane flap group and amniotic membrane + nictitating membrane flap group. To compare corneal healing, fluorescein dye test, histopathological examination and TUNEL assay were performed. The healing size of the corneal epithelium in was largest among groups and it was significantly different with the other groups (P<0.05). Also, inflammatory cell deposits and keratocyte apoptosis in amniotic membrane flap group were smallest, but the width of the corneal epithelium was thickest among groups. Therefore, we tentatively predicted that the amniotic membrane flap would be an alternative effective method for the treatment of superficial canine corneal ulcer.