In this study, we isolated and phenotypically identified 108 yeast strains from various clinical specimens collected from 100 hospitalized patients at three tertiary hospitals in São Luís-Maranhão, Brazil, from July to December 2010. The isolates were analyzed for their susceptibility to four of the most widely used antifungal agents in the surveyed hospitals, amphotericin B, fluconazole, 5-flucytosine and voriconazole. The species identified were Candida albicans (41.4%), Candida tropicalis (30.1%), C. glabrata (7.4%), Candida parapsilosis (5.5%), Candida krusei (4.6%), Cryptococcus neoformans (4.6%), Trichosporon spp . (3.7%), Candida norvegensis (0.9%), Rhodotorula glutinis (0.9%) and Pichia farinosa (0.9%). A higher isolation rate was observed in the following clinical specimens: urine (54 isolates; 50%), respiratory tract samples (21 isolates; 19.4%) and blood (20 isolates; 18.6%). Candida albicans isolates were 100% sensitive to all antifungal agents tested, whereas Candida krusei and Crytococcus neoformans displayed intermediate resistance to 5-flucytosine, with Minimal Inhibitory Concentration (MIC) values of 8 mg/mL and 16 mg/mL, respectively. Both strains were also S-DD to fluconazole with an MIC of 16 mg/mL. C. tropicalis was resistant to 5-flucytosine with an MIC of 32 μg/mL. This study demonstrates the importance of identifying the yeast species involved in community and nosocomial infections.