Bioaerosols generated at composting plants are released during processes that involve vigorous movement of material: fresh waste delivery, shredding, compost pile turning, screening. Bioaerosols are a cause of concern because of their potential impact on the health of workers and residents living close to such facilities due to the presence of thermophilic actinomycetes, molds, endotoxins and 1-3 β-glucans. Using 16S rRNA and 18S rRNA molecular inventories, the microbial signature of composting aerosols was defined and gave us access to microbial indicators strongly associated with compost. Quantitative PCR systems were designed for two phylotypes: one targeting Saccharopolyspora rectivirgula and relatives and one targeting a phylotype belonging to the Thermoactinomycetes. The indicators were validated by comparing their concentrations in impacted samples to their background levels in natural environments. Their concentration in compost during a whole process was monitored in two composting facilities treating different types of waste, as well as their levels in aerosols emitted during operational activities. Sampling campaigns were then performed (13 days of measurements) on both sites to analyze the dispersal of bioaerosol emitted during turning and screening activities by monitoring the indicators on-site and at increasing distances downwind. The impact of the concentration at the emission point and of meteorological conditions was analyzed. Finally, the particle-size distribution of airborne bacteria and of the indicator affiliated to Saccharopolyspora rectivirgula and relatives were determined by qPCR using samples from an Electrical Low Pressure Impactor. The results showed that single-bacterial cells are predominant in aerosols emitted by the composting facility investigated.