Although fungal infections participate significantly to human morbidity and mortality, the efficacy of these diseases on human health is not appreciated. Diagnosing fungal infections is a challenge, particularly in the immunocompromised host. Signs and symptoms are nonspecific, colonization is difficult to identify from invasive disease, blood cultures (BC) are commonly negative, and patients are often unable to undergo invasive diagnostic procedures. Culture and microscopic examination remain the "gold standard" but are insensitive. Antigen assays such as the glucan and galactomannan detection systems are mostly used. However, these tests vary in sensitivity and specificity, depending on the patient population involved. Molecular-based assays are not yet clinically validated، however Advances in molecular technology show great potential for the quick detection and identification of fungi for medical, scientific and commercial purposes. However, some new methods such as MALDI-TOF MS has become the standard method for routine identification of most microbial organisms in clinical laboratories and have largely replaced biochemical assays.