Background: Candida species (Candida spp) has been increasingly emerging nosocomial pathogens with increasing treatment failure, so it is important to isolate, identify the species and check the sensitivity pattern. Fluconazole resistance is linked to multiple molecular pathways demonstrated by Candida spp. Objective: To determine the frequency of Candida spp. isolated from a variety of clinical samples, antifungal susceptibility patterns and detection of fluconazole-resistant genes expression pattern. Methodology: A cross-sectional study was performed on 300 various clinical samples in a hospital setting from patients attending Outpatient and Inpatient departments of Tanta University hospitals. Several candida spp. was identified at species level by using conventional tests, and VITEK 2 compact system. Antifungal susceptibility testing was carried out using VITEK 2 compact automated system and disk diffusion method followed by detection of gene expression pattern for ERG11, and efflux pumps by Real-time- PCR in candida species resistant to fluconazole. Results: From 300 clinical samples, 51 different species of candida were identified. Non albicans candida (NAC) were more   prevalent (56.9%) than C. albicans (43.1%). Overall, the isolated candida species 20 (39.2%) were resistant to fluconazole. Regarding to gene expression pattern Ergosterol (ERG11), Candida drug resistance (CDR1, CDR2), Pleiotropic drug resistance (PDR1) in C. glabrata, there was a statistically significant difference in the ERG11, CDR1 expression levels only in resistant isolates compared to sensitive isolates. while analysis of gene expression of C. auris efflux pump (CDR1, CDR2), Multidrug resistance (MDR1) and ERG11, revealed statistically significant differences in all tested genes. Conclusion: There was increase in the frequency of non albicans Candida (NAC) and emergence of fluconazole resistant species; C. auris emerged during pandemic of COVID-19 and they significantly exhibit expression levels higher than C. glabrata.