Proteus anguinus is a neotenic cave amphibian endemic to the Dinaric Karst and represents a symbol of Slovenian natural heritage. It is classified as 'Vulnerable' by the International Union for Conservation of Nature (IUCN) and is one of the EU priority species in need of strict protection. Due to inaccessibility of its natural underground habitat, scientific studies have been primarily conducted on Proteus in captivity where amphibians may be particularly susceptible to opportunistic microbial infections. In this case report, we present the results of an analysis of an individual that had been kept in captivity for 6 yr and then developed clinical symptoms, including ulcers, suggesting opportunistic microbial infection. Pigmented fungal hyphae and yeast-like cells were present in the dermis and in almost all other sampled tissues. Sampling of the ulcer allowed the isolation of a diverse array of bacterial and fungal species. We identified the water-borne, polymorphic black yeast Exophiala salmonis, an opportunistic pathogen of fish, as the cause of the primary infection. This is the first report on a fungal infection of Proteus and on cave salamanders in general.