Background: Systemic candidiasis has been on the rise in recent years due to the increasing number of patients with malignancies and use of immunosuppressants. The present study seeks to identify the distribution of Candida species isolated from malignant patients and determine in vitro antifungal susceptibility patterns of the isolates to promote their effective management. Methods: Blood and urine samples from 385 patients with malignancies were cultured. Identification and susceptibility patterns of the Candida isolates from clinical samples to antifungal drugs were done using API 20C AUX system and microdilution methods. Results: From 90/385 patients (23.4%), 102 Candida spp. were isolated. The most prevalent species was Candida albicans with sensitivity rates of 91%, 96%, 100%, 96%, and 60% to fluconazole, amphotericin B, caspofungin, voriconazole, and itraconazole, respectively. Epidemiological cutoff values for amphotericin B and voriconazole were 0.064 and 0.032, respectively. All the isolated species were of wild-type for all antifungal agents except 4% of Candida albicans, which were non-wild type to amphotericin B and voriconazole and 6% to itraconazole. No relationship was seen between the rate of isolated species and sex, age, and the type of malignancy; but the relationship between the use of antibacterial agents and Candida isolation was significant (P < 0.05). Conclusions: Mutations in drug sensitivity were found in some species (non-wild type). As there was a relationship between the use of antibacterial agents and the isolation of Candida species from immunocompromised patients, accurate diagnosis of Candida species isolated and their antifungal susceptibility patterns are needed for the management of such patients.