A premature neonate, requiring prolonged hospitalization, intensive care, multiple surgeries, and broad-spectrum antibiotics, developed a systemic fungal infection. Initial blood cultures identified a Candida species, later confirmed as Candida berthetii through molecular sequencing. The infant received antifungal treatment with amphotericin B and fluconazole, eventually recovering. This case represents the first documented human systemic infection by C. berthetii, highlighting the diagnostic challenges of emerging fungal pathogens in vulnerable populations like preterm infants. Teaching point: Advanced molecular diagnostics are crucial for identifying rare or emerging pathogens, especially in immunocompromised patients where timely and accurate diagnosis can significantly impact treatment and outcome.