Emerging infectious fungal diseases such as chytridiomycosis, caused by Batrachochytrium dendrobatidis and B. salamandrivorans in amphibians, or ophidiomycosis in reptiles (Ophidiomyces ophiodiicola), are major threats that can drive species or entire populations to extinction over a short period of time. Besides these well-documented pathogens, such diseases can be caused by numerous opportunistic fungal species that can target e.g. immunocompromised individuals from various species of vertebrates. In reptiles, opportunistic species are mainly documented in captive animals kept in inadequate conditions, but data remains scarce for wild individuals. In the present study, we isolated and genetically identified fungal species responsible of skin lesions in wild-caught smooth snakes (Coronella austriaca) during a field survey targeting endangered reptile species in Switzerland. A total of 18 fungal species were isolated and genetically identified from the lesions of the two wild-caught snakes and included several species known for being opportunistic pathogens in vertebrates and infecting mainly immunocompromised individuals, such as Alternaria infectoria and Rhodotorula spp. It is not possible to establish whether the snakes had such an issue. However, the exceptional wet and cold conditions experienced in spring 2021 might have trigger the infections. Indeed, high humidity has been recorded as a predisposing factor for mycoses in captive reptiles.