A 1-year-old female yellow-eyed penguin (Megadyptes antipodes) was diagnosed with chronic discospondylitis on the basis of clinical signs and results of hematologic tests, radiography, and computed tomography. Despite significant destruction of the affected vertebral bodies and gross malformation of the spine, neurologic function was unaffected. Treatment with antibiotics, antifungals, and swimming physiotherapy was attempted, but the bird died after 40 days of hospitalization. Histopathologic lesions observed at necropsy were severe chronic discospondylitis, chronic granulomatous tracheitis, proventricular ulceration, and adrenal hemorrhage. The suspected inciting cause of the discospondylitis was a reported population-wide oral stomatitis that affects yellow-eyed penguin chicks.