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Given the growing concerns over human and animal health issues related to confined animal feeding operations, an in‐depth examination is required to monitor for airborne bacteria and associated antibiotic resistance genes. Our 16S rRNA‐based pyrosequencing revealed that the airborne microbial community skewed towards a higher abundance of Firmicutes (> 59.2%) and Bacteroidetes (4.2–31.4%) within the confinement buildings, while the office environment was predominated by Proteobacteria (55.2%). Furthermore, bioaerosols in the confinement buildings were sporadically associated with genera of potential pathogens, and these genera were more frequently observed in the bioaerosols of pig and layer hen confinement than the turkey confinement buildings and office environment. High abundances of tetracycline resistance genes (9.55 × 10² to 1.69 × 10⁶ copies ng⁻¹ DNA) were also detected …