Tuberculosis (TB) is caused by pathogenic species within the Mycobacterium tuberculosis complex (MTBC). In the present case, a 40-year-old African man was admitted acutely. Despite negative microscopy, anti-TB treatment was initialized. Thirteen hours after hospitalisation, the patient suffered circulatory failure and died. Post mortem material from the lungs and pericardia tested positive for MTBC and was identified as Mycobacterium africanum by a new molecular method that enables identification of six of the eight MTBC species and provides clinicians with species-specific results.