An adult female Aldabra giant tortoise (Geochelone gigantea) was found dead with a 2 month-history of decreased appetite. At necropsy, multiple ulcers were seen in the mucosa of stomach and colon. Histopathologically, the ulcers were characterized by extensive necrosis, hemorrhage, and marked edema, along with numerous chlamidospores and aseptate fungal hyphae. Fungal structures infiltrated into the lamina propria, submucosa and muscle layer; their invasion into blood vessels formed thrombosis. Immunohistochemically, the fungal structures were strongly positive with an antibody against Candida spp. This case is the first report on gastrointestinal candidiasis in an Aldabra giant tortoise.