The atmosphere harbours a vast diversity of primary biological aerosols (PBAs) that are subjected to vertical and horizontal dispersal mechanisms that are not fully understood. In addition to size and weight constraints on PBAs to be lifted into the air column, local meteorological features dominate the fate of bioaerosols and their possible inclusion in long‐range transport. For organic particles to be included into long distant dispersal, they have to overcome surface vertical mixing of the planetary boundary layer (PBL) to reach levels of laminar air movement. Hence, the biogeography of PBAs along a vertical distribution through the PBL needed further study. To assess the microbial biodiversity along an altitudinal gradient, air samples were collected between 1,000 and 3,100 m above sea level at Mount Sonnblick in the Austrian Alps. 16S rRNA gene and internal transcribed spacer sequencing for bacteria and fungi, respectively, were used to define distinct microbial communities that were separated by the PBL. Up to the top of the PBL, plant‐associated bacteria and fungi were detected and were subjected to limited vertical dispersal due to size‐constraints. This indicates that those communities become aerosolised but were not lifted into higher altitudes. However, a variety of ubiquitous, thermophilic strains that are often identified with heavy dust events and high endurance towards extreme conditions were significantly increased (relative abundance) at higher elevations. The lack of information on vertical dispersal is due to reliance on ground‐based investigations that bias the interpretation of dispersal dynamics. Thus, to understand the mechanisms for near‐ground communities to become airborne and subsequently included in long‐range transport, we recommend investigating meteorological driving forces for an improved biogeographical assessment. Here, we show, for the first time, an assessment of the biogeography of bacterial and fungal assemblages along a vertical alpine air column transect.