A 59-year-old man with a long history of under-treated diabetes mellitus presented with severe inflammation that had spread from the sinus to the left orbital cavity. The bilateral internal carotid arteries were severely stenotic, causing multiple infarctions in the brain parenchyma. There was no β-D-glucan detected in the cerebrospinal fluid. Based on the presence of central nervous system (CNS) inflammation and vascular involvements that spread from the sinusitis, we tentatively diagnosed this patient as having invasive fungal CNS infection, i.e. zygomycosis or aspergillosis. Although the patient was treated with anti-fungal drugs such as liposomal amphotericin B and voriconazole, he died of respiratory failure. Pathological examination of the autopsied tissues demonstrated zygomycosis in the brain and heart. The prevalence of zygomycosis is generally very low (-5% of CNS infections) compared with that of other fungal infections. The lack of an appropriate diagnostic marker may lead to the under- or mis-diagnosis of zygomycosis. Moreover, it is hard to differentiate zygomycosis from aspergillosis because the two diseases share common clinical features such as the association of sinusitis and vascular involvement. The clinically diagnostic points that discriminate zygomycosis from aspergillosis are as followed; i) β-D-glucan is negative in zygomycosis but positive in aspergillosis; ii) diabetes is more frequent in patients with zygomycosis to those with aspergillosis; iii) the infectious lesion in aspergillosis shows an iso-low-intensity on T(2) weighted MRI image but shows a high intensity lesion in zygomycosis. The mortality rate of CNS zygomycosis is so high that an early diagnosis of it is warranted and the start appropriate anti-fungal treatments or surgical drainage in the early stage of the disease.