Cryptococcus species are environmental basidiomycetous yeasts, with a worldwide distribution and remarkable environmental adaptation. Although many species do not cause disease, C. neoformans and C. gattii are the causative agents of cryptococcosis, a life-threatening infection and a significant public health problem worldwide. Infection affects especially immunocompromised individuals, both animals and humans alike. In wildlife, cryptococcosis appears to be more prevalent in captive populations. Using cultural and molecular methods, we studied yeasts isolated from nasal swabs collected from 130 free-ranging quokkas (Setonix brachyurus) on Rottnest Island and the mainland of Western Australia. We isolated C. neoformans var. grubii (serotype A) and C. magnus from the nasal lining of apparently healthy S. brachyurus from Rottnest Island, only. A total of seven cryptococcal isolates were recovered (7.2%, 7/97). Cryptococcus neoformans var. grubii was recovered from two animals (2.1%, 2/97), C. magnus from one animal (1.04%, 1/97), while unspeciated Cryptococcus spp. were recovered from four (4.12%, 4/97). C. neoformans var. grubii and C. magnus were recovered from animals in human-populated areas on Rottnest Island. Other recovered fungal organisms were: Rhodotorula glutinis, R. mucilaginosa, Aureobasidium pullulans, and Rhodosporidium kratochvilovae. There were no significant associations between the presence of other concomitant organisms (i.e. herpesvirus, piroplasms, Salmonella, microfilariae, nematode eggs, Eimeria spp.) with the presence of Cryptococcus, and no significant effect of C. neoformans var. grubii on the haematology, blood chemistry or peripheral blood cell morphologies was observed. To the best of our knowledge, this is the first documented isolation of C. neoformans var. grubii (serotype A) and C. magnus in a free-ranging macropod in Western Australia. The recovery of C. neoformans var. grubii from quokkas suggests the presence of an environmental source on Rottnest Island, and constitutes an important finding for public health and management of wild and captive S. brachyurus.