We report a case of cerebral mucormycosis in a 28-year-old male who was affected by chronic myeloid leukaemia and underwent allogeneic bone marrow transplantation. Nine months post-transplantation, he was admitted to the hospital with fever, bilateral eyelid oedema and neutropenia. X-ray analysis showed numerous areas of pulmonary parenchymal thickening, and a computed tomography scan of the brain showed inflammation of the frontal, maxillary, ethmoidal and sphenoidal sinuses and diffuse swelling of the periorbital tissues. Sinus cultures were taken, and based on its characteristic rhizoid structure, we classified the isolated fungus as a member of the genus Rhizopus. The fungus was identified as an Rhizopus oryzae species, as assessed by sequencing of the internal transcribed spacer of the rRNA gene. Treatment with amphotericin B was ineffective, however, and the patient died 2 weeks after admission. This case highlights the potential severity of an invasive infection of R. oryzae, identified by molecular biology techniques.