Twenty-two raptors from a rehabilitation centre were evaluated for the presence of yeasts prior to returning them to the wild, and the recovered Candida isolates were tested for in vitro antifungal susceptibility and phospholipase production. Samples were collected from the crop/lower esophagus and cloaca. In vitro antifungal susceptibility and phospholipase production of 21 Candida strains were assessed through broth microdilution and growth on egg yolk agar respectively. Twenty-seven isolates, belonging to seven species, were recovered from 16 tested birds, with C. albicans and C. famata as the most prevalent species. Three out of 21 isolates (2 C. albicans and 1 C. tropicalis) were simultaneously resistant to fluconazole and itraconazole. As for phospholipase production, 8 (8/21) isolates (6 C. albicans, 1 C. famata and 1 C. parapsilosis) showed enzymatic activity. The most relevant finding in this study was the isolation of resistant Candida spp. from wild raptors that had never been submitted to antifungal therapy, which suggests exposure to environmental contaminants. Based on this, we propose the assessment of Candida spp. from the gastrointestinal tract of raptors as a tool for environmental monitoring.