Culture-based pathogen identification in skull base osteomyelitis, particularly for fungi, is often inaccurate. We report the case of patient with fungal skull base osteomyelitis cured by sustained antifungal therapy after 16 months of debilitating illness. Due to medical complications, a strong clinical rationale was needed to justify long-term antifungal therapy. The offending fungus was identified by experimental molecular technology (Ibis T5000 universal biosensor); invasive fungal disease was corroborated by biochemical assays. Our discussion will help familiarize the otolaryngologist with existing biochemical and molecular diagnostics for invasive fungal disease. We encourage future investigators to study their application in cases of skull base osteomyelitis.