Background: The introduction of MALDI-TOF MS, BD PHOENIX, and VITEK-2 equipment into the clinical microbiology laboratory has changed the techniques of fungal identification. This technique can be used to find cryptic species that have critical susceptibility patterns. The MALDI-TOF MS, BD PHOENIX, and VITEK-2 systems were used to identify clinical strains. Assuming MALDI-TOF MS isolate identification as standard, discrepancies between three approaches were evaluated. Finally, these isolates were subjected to in vitro susceptibility testing. Results: The agreement between the two approaches for 498 yeast isolates was 93.6 percent (32 discrepant isolates). The BD PHOENIXconcordance with VITEK-2 systems was lower than MALDI-TOF MS. Several of these discordant yeasts had high antifungal agent MICs.