Cutaneous fungi are known to affect parts of the outermost skin layers of mammals, including the epidermis, stratum spinosum and stratum corneum, as well as mucocutaneous membranes, genitalia or external ears. Relatively little is known about fungal infections of Mysticete cetaceans and studies are needed to determine the fungal diversity associated with these marine mammals. This case report was aimed at identifying the fungi associated with the skin of a diseased neonatal southern right whale (Eubalaena australis) found stranded in the Western Cape Province of South Africa. Initial physical examination on site revealed hyperplasia of the follicular and epidermal epithelium. Preliminary examination of skin biopsies using scanning electron microscopy indicated that the skin was colonized by fungal hyphae. Isolation methods yielded a number of fungal isolates, which were identified using standard morphology and rDNA sequence data. These analyses confirmed colonization of the cutaneous layers by species belonging to the genera Fusarium, Chaetomium and Penicillium. Moreover, all isolates were capable of degrading keratin, indicating that skin may act as a natural substrate for these fungi. This study is the first report of the association of these fungi with southern right whale skin.