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Employees at agricultural working places are often exposed to complex bioaerosols. Investigations of bioaerosols in duck houses revealed concentrations of cultivable bacteria between 0.4 and 3 × 105 colony forming units (CFU) m−3 on tryptone soy agar, 0.3 and 2 × 105 CFU m−3 on actinomycetes isolation agar, and 0.8 and 5 × 103 CFU m−3 on Middlebrook agar, respectively, when incubated at 25°C. At an incubation temperature of 37°C, 0.6–3 × 102 CFU m−3 were counted on MacConkey agar and 0.3–2 × 103 CFU m−3 on Middlebrook agar, and the concentrations of bacteria on glycerol–arginine agar and oatmeal agar incubated at 50°C varied between 0.1 and 2 × 103 and 1 and 7 × 103 CFU m−3, respectively. In addition, high concentrations of cells were observed by fluorescence microscope quantification of cell counts after 4′,6-diamidino-2-phenylindol staining with 3–8 × 107 cells m−3. A total of 213 colonies with different morphological appearance were selected and the isolated pure cultures were identified at the genus level using the 16S rRNA gene sequence analyses. In summary, 19 different genera of Actinobacteria, four genera of the Firmicutes, one genus of the Bacteroidetes, and five genera of the Proteobacteria were identified. Several isolates represent new phylogenetic lineages. Based on 16S rRNA gene analyses, some isolates were most closely related to Cellulosimicrobium funkei, Corynebacterium falsenii, Corynebacterium xerosis, Mycobacterium arupense, and Staphylococcus epidermidis, which have been grouped into Risk group 2 of biological agents and may cause negative pulmonary health effects. These bacterial species were present in high concentrations up to 104 CFU m−3. For this reason, we recommend an adequate personal breathing protection at these working places.