The objective of the study is to investigate the distribution patterns of airborne bacteria and fungi in three feedstuff-manufacturing factories in Korea. The geometric mean (±GSD) levels of airborne bacteria and fungi in the feedstuff-manufacturing factory were 113(±18) cfu/m3 and 89(±5) cfu/m3 for pelleting process and 198(±5) cfu/m3 and 124(±12) cfu/m3 for powdering process, respectively. The percentage of respirable (0.65–4.7 μm) and total (>4.7 μm) concentration of airborne bacteria and fungi in the feedstuff-manufacturing factory ranged from 60% to 90% and were higher in pelleting process than powdering process. The ratio of indoor concentration and concentration in ventilation air from outside for airborne bacteria and fungi exceeded 1.0 regardless of types of feedstuff manufacture process. The predominant airborne microorganisms in the feedstuff-manufacturing factory were Staphylococcus spp., Micrococcus spp., Corynebacterium spp. and Bacillus spp. for airborne bacteria and Cladosporium spp., Penicillium spp. and Aspergillus spp. for airborne fungi, respectively. Based on the result of the study, there would be an association between relative humidity among environmental factors and airborne microorganism's bioactivity.