Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities1. Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes2,3, and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change4. One of the most pertinent biomes in this regard is Antarctica, given its geographic isolation and vulnerability to climate change and human disturbance5. Here, we report microbial diversity in near-ground and high-altitude air above the largest ice-free Antarctic habitat, as well as that of underlying soil microbial communities. We found that persistent local airborne inputs were unable to fully explain Antarctic soil community assembly. Comparison with airborne microbial diversity from high-altitude and non-polar sources suggests that strong selection occurs during long-range atmospheric transport. The influence of selection during airborne transit and at sink locations varied between microbial phyla. Overall, the communities from this isolated Antarctic ecosystem displayed limited connectivity to the non-polar microbial pool, and alternative sources of recruitment are necessary to fully explain extant soil diversity. Our findings provide critical insights into the role of airborne transport limitation in determining microbial biogeographic patterns.