Opportunistic fungal pathogens are one of the important causes of nosocomial infections, and several different types of yeasts, especially Candida species are increasingly recovered from immunocompromised patients. Since many of the yeasts are resistant to the commonly used antifungal agents, the introduction of appropriate therapy depends on rapid and accurate identification. The aims of this study were to compare the commercial identification systems namely API® ID 32C (bioMerieux, France) and Phoenix™ Yeast ID Panel (Becton Dickinson Diagnostics, USA) for the identification of Candida species and to evaluate the effect of morphological findings in the identification process. A total of 211 yeast strains isolated from different clinical samples (111 urine, 34 blood/vascular catheter, 27 upper/lower respiratory tract, 16 abscess/pus, 13 throat/vagina swabs and 10 sterile body fluids) of 137 patients hospitalized in Uludag University Health and Research Center between October 2013 to January 2014, were included in the study. Samples were cultured on blood agar, chromogenic agar (CHROMagar Candida, BD, USA) and Saboraud's dextrose agar (SDA), and isolated yeast colonies were evaluated with germ tube test and morphological examination by microscopy on cornmeal/Tween-80 agar. The isolates were identified as well by two commercial systems according to the manufacturers' recommendations. Discrepant results between the systems were tried to be resolved by using morphological characteristics of the yeasts. Of the isolates 159 were identified identical by both of the systems, and the concordance between those systems were estimated as 75.4%. According to the concordant identification, the most frequently isolated species was C.albicans (44.1%) followed by C.tropicalis (9.9%), C.glabrata (9.5%), C.parapsilosis (8.5%) and C.kefyr (8.1%). The concordance rate was 81.7% in identification of frequently isolated species (C.albicans, C.tropicalis, C.parapsilosis, C.glabrata, C.kefyr), however it was 38.7% for the rarely isolated ones (C.krusei, C.lusitaniae, C.inconspicua/C.norvagensis, C.catenulata), representing statistical significance (p= 0.034; x2 test). Although not significant (p= 0.31; x2 test), the rate of concordance was increased (88.1%), when adding the morphological findings to the identification process. Of 211 isolates 37 (17.5%), 50 (23.7%) and 124 (58.8%) were identified according to their growth characteristics on chromogenic agar, blood agar and SDA, respectively, indicating no statistically significant difference between the media (p> 0.05). Although genotypic identification is essential, phenotypic methods are more commonly used in routine laboratories for the identification of yeast species. However, since genotypic identification could not be performed in this study, none of the systems were accepted as the standard method and therefore the sensitivity and specificity of the systems were not calculated. On the other hand, our data indicated that the two identification systems were comparable and careful observation of yeast morphology could add confidence to the identification. In conclusion, since the Phoenix™ Yeast ID system was found more practical with easier interpretation, and the results were obtained earlier than those of the API® ID 32C system (16 hours versus 48 hours), it was thought that Phoenix™ Yeast ID system may be used reliably in the routine laboratories. However, as none of the methods evaluated was completely reliable as a stand-alone, careful evaluation is necessary for species identification.