Opportunistic infections, including mycotic diseases, are increasingly being recognized as a major public health concern in Southeast Asia. The diagnosis of fungal infections from clinical specimens relies mainly on culture and, at select institutions, molecular methods. In certain instances, it is possible to detect fungal elements, such as hyphae and yeast forms, in tissue samples submitted to the histopathology laboratory. Routine examination with hematoxylin and eosin (H and E) staining is sufficient to detect the presence of organisms in most cases. On occasion, special stains such as periodic acid-Schiff (PAS) and Gomori methenamine silver (GMS) may be utilized to highlight fungal structures. Definite species identification of fungi detected on routine histology still relies on correlation with clinical findings and ancillary tests. Among the challenges encountered in the region are the lack of facilities, equipment, and supplies in regular diagnostic laboratories; overreliance on referral laboratories; lack of skilled laboratory personnel; and few opportunities for training and subspecialization in diagnostic mycology. The introduction of newer techniques, such as MALDI-TOF and nucleic acid-based tests, may augment the services related to fungal diagnosis on biopsy specimens. Furthermore, international linkages in the region, especially in tropical medicine, may pave the way toward enhancing mycology services in the region.