The incidence of fungal infections, particularly those caused by Candida species, has significantly risen among immunocompromised patients in recent years. Aim: This study evaluated the species distribution, antifungal susceptibility patterns, and virulence gene profiles of Candida species isolated from critically ill ICU patients while comparing the diagnostic performance of conventional phenotypic isolation media with molecular genotypic identification methods. Materials and Methods: A total of 211 clinical specimens were obtained from 200 hospitalized patients at Menoufia University Hospitals, Egypt. Candida species were phenotypically identified using cornmeal agar supplemented with Tween 80 (CTA) and CHROMagar^TM Candida (CMA) and were molecularly confirmed at the species level by sequencing PCR-amplified ITS regions. Antifungal susceptibility profiles to fluconazole, voriconazole, and amphotericin B were evaluated using the disk diffusion method. Furthermore, real-time PCR was deployed to detect genes encoding adherence factors and Secreted Aspartyl Proteinase. Results: Candida species were recovered from 45 out of 211 clinical specimens. The most frequently isolated species was Candida albicans (15/45, 33.3%), followed by C. parapsilosis (9/45, 20.0%), C. glabrata (7/45, 15.5%), C. tropicalis (7/45, 15.5%), C. krusei (4/45, 8.8%), and C. famata (3/45, 6.7%). Among the recovered Candida isolates, the percentage rates of the ALS1, ALS3, HWP1, and SAP4 genes were 40%, 42.22%, 44.4%, and 37.78%, respectively. HWP1 was the most frequently detected pathogenicity factor, whereas SAP4 was the least prevalent. Conclusions: In the studied immunocompromised cohort, non-albicans Candida species constituted a substantial proportion of clinical isolates. Notable antifungal resistance patterns were also observed, emphasizing the value of integrated phenotypic and genotypic identification for tailored management. Furthermore, virulence-associated genes (ALS1, ALS3, HWP1, and SAP4) were detected in isolates of several Candida species, highlighting their presence in clinical strains.