An adult male Aldabra tortoise (Geochelone gigantea) presented with a deep flaking area of the carapace, and histologic examination of biopsies from this area revealed phaeohyphomycosis of the superficial keratinized layers. The disease progressed rapidly and spread to numerous sites on the carapace. After several weeks of regular debridement, deep bone involvement was evident and was confirmed through histologic examination. Fungal culture was attempted but was unsuccessful at isolating the infectious agent. Polymerase chain reaction analysis of extracted DNA from the fixed tissue block identified the fungus as Exophiala oligosperma. Initial treatment included weekly debridement and oral and topical antifungal agents. A nuclear scintigraphy bone scan was performed to determine the extent and status of the infection. Multiple foci of uptake of the radiopharmaceutical marker were present within the carapace, indicating active lesions. The tortoise was maintained on oral antifungal treatment, and lesions resolved over several months. A repeat bone scan performed 1 yr after initial presentation showed reduction in marker uptake, indicating a response to treatment in the deeper lesions. Phaeohyphomycosis should be considered as a differential diagnosis for cases of shell lesions in chelonians.