Background: Candida infections are commonly treated with fluconazole. Efflux pumps are one of the mechanisms for fluconazole resistance. This study assessed the accuracy of identification of Candida species with reduced fluconazole susceptibility and their relative expression of major efflux pump genes. Methods: Candida species (n=111) were collected from clinical samples, identified by Brilliance Candida Agar (BCA) and germ tube test, then tested for fluconazole susceptibility by disk diffusion. Confirmation of identification and susceptibility to fluconazole was done by Phoenix BD and broth microdilution methods, and the accuracy of preliminary methods was calculated. qPCR was performed to evaluate the gene expression of common efflux pump genes. Results: The most predominant were C. albicans (32%) and C. tropicalis (29%). Accuracy of BCA identification was 84% for both species. Reduced fluconazole susceptibility was detected in 8.3% of C. albicans and 40.6% of C. tropicalis. Accuracy of disk diffusion was 100% for C. albicans and 62% for C. tropicalis. qPCR showed upregulation of CDR2 efflux pump among non-susceptible C. albicans (1.99 ± 1.04), though not statistically significant. CDR1 expression was at a basal level for C. albicans (0.9 ± 0.25) and C. tropicalis (0.69 ± 0.76). MDR-1 was significantly downregulated in non-susceptible C. tropicalis (0.30 ± 0.63, p= 0.025). Conclusion: Brilliance Candida Agar  identification requires verification. The disk diffusion method is of higher accuracy with C. albicans than with C. tropicalis. Overexpression of CDR1 and CDR2 in C. albicans, and CDR1 and MDR1 in C. tropicalis were not the main reasons behind reduced susceptibility to fluconazole.