Siliceous marine microfossils were unexpectedly discovered during the analysis of flower honey samples from Poland and Tunisia. The microfossils were represented by protist with siliceous skeletons: silicoflagellates, diatoms, and endoskeletal dinoflagellates. This is the first record of such microfossils in honeys. Based on the high percent of anemophilous pollen grains and spores in the sample, it was hypothesized that silicoflagellates were deposited from the air onto the nectariferous flowers, then bees harvested them with the nectar. Based on the comparison of pollen content of honeys and flowering calendar of Tunisia, the harvest time of honey was identified as a period between 1 April and 31 May 2011. Trajectory analysis of air masses in this period confirmed that siliceous microfossils could be aerosolized by wind from the rocks of the so-called Tripoli Formation of Messinian age (6–7 Ma). Similar to the Tunisian case, the Polish trajectory simulation also supports the hypothesis of atmospheric transport of silicoflagellates from outcrops of Oligocene age in the Polish Outer Carpathians. In the case of diatom content of honey, however, the source can be both natural (wind) and artificial (diatomaceous earth filters). For a correct determination, natural sources of siliceous bioparticles, such as wind transport from nearby outcrops should be also considered. Silicoflagellates could be used as complementary indicators of the geographical origin of honeys collected in areas characterized by diatomite outcrops, supporting the results obtained with other methods; thus, such indicators merit further studies within the area of honey authenticity.