Objectives: The objective of the present study was to evaluate and compare the efficiency of a filter based sampling method and a high volume sampling method for sampling airborne culturable fungi present in waste sorting facilities. Material and Methods: Membrane filters method was compared with surface air system method. The selected sampling methods were modified and tested in 2 plastic waste sorting facilities. Results: The total number of colony-forming units (CFU)/m³ of airborne fungi was dependent on the type of sampling device, on the time of sampling, which was carried out every hour from the beginning of the work shift, and on the type of cultivation medium (p < 0.001). Detected concentrations of airborne fungi ranged 2×10²–1.7×10⁶ CFU/m³ when using the membrane filters (MF) method, and 3×10²–6.4×10⁴ CFU/m³ when using the surface air system (SAS) method. Conclusions: Both methods showed comparable sensitivity to the fluctuations of the concentrations of airborne fungi during the work shifts. The SAS method is adequate for a fast indicative determination of concentration of airborne fungi. The MF method is suitable for thorough assessment of working environment contamination by airborne fungi. Therefore we recommend the MF method for the implementation of a uniform standard methodology of airborne fungi sampling in working environments of waste treatment facilities.