A 64-year old farmer developed cough, dyspnoea on exertion, and recurrent febrile episodes. X-ray and CT scan revealed bilateral lower lobe opacities in his lungs. A transbronchial biopsy was performed and histopathological findings were interpreted as consistent with a pulmonary necrotizing clear-cell carcinoma and later as a Pneumocystis carinii pneumonia. Due to persistence of symptoms, six months later another lung biopsy was performed and a mould was cultured which was identified by 18S rDNA sequencing as Emmonsia sp. The patient showed some improvement under itraconazole treatment. This is the first description of a human infection with Emmonsia sp. in Germany.