The incidence of invasive fungal infections (IFIs) has increased owing to the rising number of immunodeficient patients. A case-control study was performed at the Ain Shams University Hospitals, Cairo, Egypt. The case group (n = 80) included 80 patients diagnosed with hematological malignancies, and the control group (n = 20) included 20 patients. All patients were tested for the presence of fungal species using blood culture and panfungal real-time polymerase chain reaction (RT-PCR). Fungal species differentiation was performed using high-resolution melting (HRM) PCR. There were 39 suspected cases of IFIs among the 80 patients. The panfungal RT-PCR detection rate was 51.3% (41/80). HRM-PCR identified that 51.2% of the fungal species were Candida albicans, 44.0% were non-Candida albicans, and 4.9% were Mucor. The blood cultures were positive for the presence of fungi in two patients with acute myeloid leukemia. The fungal detection rate using the panfungal RT-PCR technique was significantly higher than that using the blood culture technique (P < 0.001). RT-PCR using panfungal markers is sensitive, rapid, and superior to the blood culture technique to detect IFIs. HRM-PCR is a specific test for species identification.