Airborne eukaryotic communities (AEC), rank among the least studied aerobiological components, despite their adverse impacts on human health and the environment. Here, we describe the AECs in the global dust belt, the area between the west coast of North Africa and Central Asia, which supports the highest dust fluxes on the planet. We sampled atmospheric dust over 14 months (fall 2015–fall 2016) from onshore and offshore locations of the Red Sea, the only waterbody that entirely encompassed in the global dust belt. We also sampled surface water samples to determine the potential transfer of taxa across the air-sea interface. To target the eukaryotes, we performed Miseq sequencing of atmospheric dust and surface water samples. Analysis of amplicon sequencing indicates a total pool of 18,816 sequence variants (SVs). Among 33 unique eukaryotic phyla in the AEC over the Red Sea, the most dominant taxa were Streptophyta, Apicomplexa, and Ascomycota. Aerosol eukaryotes originated from various sources and formed more diverse communities than eukaryotic communities of the Red Sea surface water. AECs were dominated by phylotypes released from plant material and soils, and including taxa reported to be harmful to human health. The AEC composition was significantly influenced by sampling locations and seasonal conditions but not by the origin of the air masses nor dust loads. This work is original and uses state-of-the-art methods and very powerful NGS- bioinformatics and statistical approaches. The selected study site has high interest and it has been well chosen because of the unique combination of high loads of dust deposition, being the only fully contained seawater body in the area acting as a sink for the atmospheric dust, and the lack of riverine inputs and watershed effects empathizing the role of atmospheric inputs in the ecology of the system.