We have analyzed the bacterial community of a large Saharan dust event in the iberian peninsula and, for the first time, we offer new insights regarding the bacterial distribution at different altitudes of the lower troposphere and the replacement of the microbial airborne structure as the dust event receeds. Samples from different open-air altitudes (surface, 100 m and 3 km), were obtained onboard the National Institute for Aerospace Technology (INTA) C-212 aircrafts. Samples were collected during dust and dust-free air masses as well two weeks after the dust event. Samples related in height or time scale seems to show more similar community composition patterns compared with unrelated samples. The most abundant bacterial species during the dust event, grouped in three different phyla: (a) Proteobacteria: Rhizobiales, Sphingomonadales, Rhodobacterales, (b) Actinobacteria: Geodermatophilaceae; (c) Firmicutes: Bacillaceae. Most of these taxa are well known for being extremely stress-resistant. After the dust intrusion, Rhizobium was the most abundant genus, (40-90% total sequences). Samples taken during the flights carried out 15 days after the dust event were much more similar to the dust event samples compared with the remaining samples. in this case, Brevundimonas, and Methylobacterium as well as Cupriavidus and Mesorizobium were the most abundant genera.Airborne microbes are ubiquitous in the atmosphere 1 and are thought to play important roles in meteorological processes (i.e. clouds and snow formation or precipitation patterns alterations) 2,3 , as well as in the long-range dispersal of plant and livestock pathogens 4,5 and in the maintenance of the diversity in aquatic systems 6 . Likewise, airborne bacteria can have important effects on human health, producing allergic asthma and seasonal allergies, and could interfere in the productivity of managed and natural ecosystems 7 . Global abundance of aerial microorganisms has been estimated, based on data from terrestrial environments, to range between 10 4 to 10 6 m −3 8 . However, more recent studies, incorporating direct counting by microscopy or quantitative PCR 9 , have yielded, more accurate, higher estimates of the abundance of airborne microbes and seasonal patterns 10 . Additionally, the atmosphere is one of the most extreme environments and microorganisms inhabiting in the troposphere are exposed to higher UV radiation, desiccation, cold temperatures and nutrient deprivation than in other environments 11,12 .Several studies have also demonstrated the potential for microorganisms to be transported over long distances through the atmosphere, associated to desert dust, as a route for the colonization of new habitats 13,14 . Thus, desert dust clouds may serve not only as a source of nutrients for terrestrial plants and primary producers in nutrient depleted oceanic waters 15,16 , but may also serve as a vehicle for global transport of microorganisms, including pathogens 13,17 .The Sahara-Sahel regions of North Africa are the dominant sources of aerosolize...