Reptiles in the wild or as pets may act as spreaders of bacteria, viruses, fungi and parasites. However, studies on the mycobiota of these animals are scanty. This study investigates the occurrence of yeasts from the cloacal swabs of snakes of different origins and the antifungal profile of the isolated strains. A total of 180 cloacal samples of snakes were collected from Morocco (Group I: n = 68) and Italy (Group II: n = 112). Yeast species were biochemically and molecularly identified. A total of 72 yeast strains belonging to 13 genera, 8 from snakes in Group I and five from snakes in Group II were identified. The most frequently isolated species were Trichosporon asahii (22.2%) and Candida tropicalis (15.3%) from snakes in Group I and Debaryomyces spp. (16.7%) and Metahyphopichia silvanorum (11.1%) from snakes in Group II. Multiple azole and amphotericin B (AmB) resistance phenomena were detected among isolated yeasts. Azole multi drug resistance phenomena were detected among yeasts from Group I and Rhodotorula mucilaginosa from Group II, whereas AmB resistance phenomena among those from Group II. Data suggest that snakes may harbor pathogenetic yeasts, being potential reservoirs and spreaders of these organisms in the environment. Since the yeast species community from different groups of animals as well as their antifungal profile reflects the epidemiology of human yeast infections in the same geographical areas, the results indicate that snakes may be considered as sentinels for human/animal pathogenic microorganisms and bio-indicators of environmental quality.