Respiratory infections are a common problem among equines and occur with variable rates of morbidity and mortality. Although some fungal species are considered primary agents of respiratory tract infections in several mammals, their relevance in respiratory diseases of equines is frequently neglected. In the present study, we performed an active search for Candida spp. in the nasal cavity of horses. The presence of Candida spp. was investigated through the use of nasal swabs that were streaked on culture media. These yeasts were identified through physiological testing and their in vitro antifungal susceptibility were also characterized. The analysis of the material from the nasal cavity of 97 randomly chosen horses resulted in the isolation of Candida spp. from 35 animals (36.08%), out of which 18 (32.14%) were C. famata, 14 (25%) C. parapsilosis, 12 (21.42%) Meyerozyma guilliermondii (C. guilliermondii), 11 (19.64%) C. tropicalis and 1 (1.78%) Wickerhamomyces anomalus (C. pelliculosa). The minimum inhibitory concentration (MIC) values ranged from 0.03125-1 μg/ml for amphotericin B; and from 0.03125-> 16 μg/ml and 0.125 to > 64 μg/ml for itraconazole and fluconazole, respectively. Resistance to fluconazole and itraconazole was observed among C. tropicalis (n = 3) and C. guilliermondii (n = 1). The data show a predominance of non-C. albicans Candida species in the nasal microbiota of healthy equines, including antifungal resistant isolates, reiterating the importance of monitoring fungal pathogens in these animals.