The PathPriorID project aims to develop user-friendly tools for the rapid and accurate identification of priority pathogens in Switzerland. Species of the genera Phytophtora, Alternaria and Colletotrichum, which respectively cause late blight (on potatoes, tomatoes, asparagus, carrots, strawberry and raspberry), Alternaria leaf spot and anthracnose (on many vegetable crops and potatoes), have become problematic in our country over the past two decades. Species of these genera cannot be identified on the basis of their morphology. The only way to identify correctly these so-called cryptic species is to use a phylogentic approach. In-depth molecular characterization of these pathogens is a mandatory step to allow the development of targeted and efficient control strategies.