The diagnosis and initiation of appropriate treatment against invasive fungal infections depend upon accurate identification of pathogens by pathologists and clinical microbiologists. Histopathology is often critical in providing diagnostic insight in patients with suspected fungal infections, and such findings are incorporated into the definitions of proven or probable disease caused by certain pathogens. Such examinations can offer provisional identifications of fungal organisms, which can help guide initial therapy while laboratory results are pending. Common etiologic agents of invasive mycoses may be recognized based on morphologic characteristics observed in tissue and biologic fluids, such as those obtained from bronchoalveolar lavage and bronchial washings. However, care should be taken in the interpretation of these findings, as there may be a false sense of the ability to correctly categorize fungal organisms to the genus or species level by morphologic features alone. Studies have demonstrated discordant results between histopathology and laboratory results due to overlapping morphologic features, morphologic mimics, and sampling errors. Thus, histopathology plays an integral role in providing a differential of potential fungal pathogens but must be combined with results from laboratory studies, including cultures, antigen tests, serology, and molecular assays, in order to improve accuracy in the identification of etiologic agents of fungal infections. Inaccurate identification of the infecting organism can lead to inappropriate antifungal therapy and possibly poor clinical outcomes.