Abstract. Aerosols containing biological components can have a significant effect on human health by causing primarily irritation, infection and allergies. Specifically, airborne fungi can cause a wide array of adverse responses in humans depending on the type and quantity present. In this study we used chemical biomarkers for analyzing fungi-containing aerosols in the eastern Mediterranean region during the year 2009 in order to quantify annual fungal abundances. The prime marker for fungi used in this study was ergosterol, and its concentrations were compared with those of mannitol and arabitol which were recently suggested to also correlate with fungal spores concentrations (Bauer et al., 2008a). Back trajectory analysis, inorganic ions, humidity and temperature were used in an attempt to identify sources as well as the dependence on seasonal and environmental conditions. We found that the ambient concentrations of ergosterol, arabitol and mannitol range between 0 and 2.73 ng m⁻³, 1.85 and 58.27 ng m⁻³, 5.57 and 138.03 ng m⁻³, respectively. The highest levels for all biomarkers were during the autumn, probably from local terrestrial sources, as deduced from the inorganic ions and back trajectory analysis. Significant correlations were observed between arabitol and mannitol during the entire year except for the winter months. Both sugars correlated with ergosterol only during the spring and autumn. We conclude that mannitol and arabitol might not be specific biomarkers for fungi and that the observed correlations during spring and autumn may be attributed to high levels of vegetation during spring blossoms and autumn decomposing.