Exposure to bioaerosols associated with horse stable indoor environment and their health effects on people and horses has recently become of particular interest. Moreover, increasing frequency of recurrent airway disease (RAO) among horses made it necessary to search for the most probable causal agents of this disease and methods of their eradication. The study was conducted in two horse stables in southern Poland (Kraków and Tarnów). Particulate matter (PM2.5, PM4, and PM10) concentrations were determined photometrically, the concentration of fungal aerosol was determined by a six-stage impactor, and next generation sequencing (NGS) was used to determine fungal community composition in one of these stables. The highest PM concentrations were observed in Tarnów, but fungal aerosol levels were higher in the Kraków stable. Based on the NGS results, the three most prevalent fungal species were Wallemia sebi, Aspergillus penicillioides, and Epicoccum nigrum, all highly allergenic and potentially involved in the occurrence of RAO in horses. Spores of the detected fungi can penetrate deeply into the respiratory system. Therefore, this study suggests that examinations of particulate matter and fungal aerosol concentrations, along with species composition assessment, should be regularly conducted in horse stables.