Opportunistic fungal infections are increasing in recent years and the spectrum of pathogens also changing with the current condition. Identifying and isolating the deep-seated fungal infections will be useful. The samples of the deep-seated fungal infections were difficult to obtain and invasive procedures like bronchoscopy is required to collect samples from the distal part of the lungs, while samples collected from lung parenchyma is difficult. Therefore, the identification and diagnosis of these fungal infections are challenging.