The species of downy willow (Salix lapponum) and swamp willow (Salix myrtilloides) are extremely rare relicts among all members of the genus Salix. In Poland, they occur only in the eastern part of the Karkonosze Mountains, Masurian Lake District, and Polesie Lubelskie area. A huge threat to both species is the drainage of peat bogs and their excessive exploitation as well as diseases caused by bacteria and fungi. The present study aimed identify fungal species colonizing the aboveground organs of plants with disease symptoms and to indicate which species may pose a threat towards S. lapponum and S. myrtilloides growing under natural conditions. This research was conducted in Polesie National Park as a part of a research project by the Ministry of Science and Higher Education. Plant health assessments were carried out in natural habitats, while aboveground organs with disease symptoms were collected for laboratory mycological analysis. Colletotrichum salicis (teleomorph Glomerella salicis), Coniothyrium concentricum, Cylindrosporium salicinum, Phomopsis spp., Truncatella angustata, and Cytospora chrysosperma (teleomorph Valsa sordida) were the fungal species most frequently isolated from leaves and shoots of both willow species. The above-mentioned fungi are dangerous plant pathogens from the family Salicaceae. There were no obligatory parasites or monophagous pathogens on the aboveground organs of downy or swamp willow. Obligatory parasites may indicate a markedly low population of host plants in Polish conditions.