The yellow-eyed penguin (hōiho, Megadyptes antipodes) is one of the world’s rarest penguin species, with a population c. 4000 and a range limited to southeastern New Zealand and its subantarctic islands. Threats to the species include habitat loss, introduced predators such as mustelids, and emerging infectious diseases. The New Zealand Department of Conservation and community groups have monitored this species since the 1980s. During the last decade several significant and distinct disease entities have emerged within yellow-eyed penguin chicks. A major entity is diphtheritic stomatitis, an idiopathic disease marked by ulceration and proliferative stomatitis of the bill commisures and oropharynx. Diphtheritic stomatitis was first identified in two chicks during the 1999/2000 breeding season, and has since spread to affect all known breeding sites on the Otago Peninsula and in North Otago. The disease spread in conjunction with histopathological features suggest an infectious aetiology. In an effort to better understand the disease, we analyse 15 years of nest-monitoring data to describe the basic epidemiology of the disease and identify risk factors. Our goal with this study is to increase the body of knowledge about diphtheritic stomatitis with a view to improving disease management in the field.