Allergic fungal sinusitis is a non-invasive disease characterized by pansinusitis with nasal polyps, with most causative agents being members of the dematiaceous fungi. Reported herein is the ninth Japanese case of allergic fungal sinusitis; an Alternaria species was culturally identified as the etiological agent. The present patient, a 32-year-old man, presented with multiple sinusitis and nasal polyps. Allergic mucin, which is a histological hallmark of this disease, was examined intraoperatively on frozen section. Although characteristic histology, including laminated masses of mucin and aggregates of eosinophils, was seen in HE-stained sections, fungal hyphae were scarce and recognized merely as clear spaces. Because fluorescent stilbene derivatives seem useful for the rapid detection of fungi, Fungiflora Y, a commercially available staining kit that includes a fluorescent stilbene derivative, was applied to the sections, and hyphae were successfully visualized using a fluorescence microscope. This stain takes only several minutes to perform. It is concluded that Fungiflora Y should be used when fungal elements are hard to find on HE stain, especially in cases in which rapid detection of fungus is requested.