Objectives: Air quality in the stables is characterized by elevated level of dust and aeroallergens which are supposed to directly cause or exacerbate several respiratory disorders. The most often recognized problem is recurrent airway obstruction (RAO), previously known as chronic obstructive pulmonary disease (COPD). There is some indication that aeroallergens (among them endotoxins) may also cause inflammation in human airways and may exceed safe levels in stables. Monitoring studies have covered mainly the determination of the concentration of respirable particles and of culturable fungi and their toxins. However, these particles do not only directly affect the respiratory system, but might act as a carrier conveying toxic contaminants and biological agents such as bacteria. In a typical, 20-horse Hungarian stable, microbial community of respirable fraction of resuspended dust has been characterized to reveal if these particles convey hazardous pathogenic bacteria, posing risk to either horses or staff. Material and Methods: Resuspended dust was sampled using a mobile instrument. The instrument contains a PARTISOL-FRM model 2000 sampler that was operated at a flow rate of 16.7 l/min and a cyclone separator which collected the particulate matter with an aerodynamic size between 1 μm and 10 μm (PM_1–10) fraction. Microbial taxa were identified by culture-independent next generation sequencing (NGS) of variable 16S ribosomal ribonucleic acid (rRNA) gene regions. Results: In total, 1491 different taxa were identified, of them 384 were identified to species level, 961 to genus level. The sample was dominated by common ubiquitous soil and organic material-dwelling taxa. Conclusions: Pathogens occurred at low abundance, and were represented by mostly facultative human pathogens, with the prevalence of Staphylococcus species.