The domesticated apple (Malus domestica Borkh.) is the most significant pome fruit grown and consumed worldwide. China is the largest producer, followed by the United States, on a global scale. However, fungal plant pathogens cause significant economic losses in the field and during storage, leading to poor fruit quality. Several pathogens also produce mycotoxins that are harmful to human health. Advancements in biological, chemical and cultural controls have been made and integrated to increase production, maintain fruit quality and enhance sustainability. In this chapter, an introduction of apple production and storage is presented, followed by discussions of the main pre- and postharvest apple pathogens, methods on integrated disease management and emerging diseases.