The presence of airborne cyanobacteria and microalgae as well as their negative impacts on human health have been documented by many researchers worldwide. However, studies on cyanobacteria and microalgae are few compared with those on bacteria and viruses. Research is especially lacking on the presence and taxonomic composition of cyanobacteria and microalgae near economically important water bodies with much tourism, such as the Adriatic Sea region. Here, we present the first characterization of the airborne cyanobacteria and microalgae in this area. Sampling conducted between 11th and 15th June 2017 revealed a total of 15 taxa of airborne cyanobacteria and microalgae. Inhalation of many of the detected taxa, including Synechocystis sp., Synechococcus sp., Bracteacoccus sp., Chlorella sp., Chlorococcum sp., Stichococcus sp., and Amphora sp., poses potential threats to human health. Aside from two green algae, all identified organisms were capable of producing harmful metabolites, including toxins. Moreover, we documented the presence of the cyanobacterium Snowella sp. and the green alga Tetrastrum sp., taxa that had not been previously documented in the atmosphere by other researchers. Our study shows that the Adriatic Sea region seems to be a productive location for future research on airborne cyanobacteria and microalgae in the context of their impacts on human health, especially during the peak of tourism activity.