Cave air, bat guano, and swabs of bat fur from caves with bat guano in Romania were analyzed by using RIDAHCOUNT cultivation plates and standard selective media for Staphylococcus and Streptococcus. 7 CFU/g). The gravity-settling principle was applied to sample airborne microorganisms, and a new method was developed for evaluation of aerosolization potential. In cave air, the concentration of total bacteria was higher than yeast and molds. In addition to coliforms, enterobacteria, E. coli, and unidentified cultivable bacteria in the air samples, we also identified Chryseomonas luteola, Klebsiella pneumoniae, Micrococcus, Salmonella, Staphylococcus, and Streptococcus. In the experiment that provoked microbial aerosolization from guano, 3.35% of total cultivable fungi were aerosolized, up to 0.10% of bacteria, and 0.00% of E. coli. The concentration of Staphylococcus in the air exceeded counts of Streptococcus. The highest concentrations of airborne microorganisms were on the ground level. Using cultivation plates as a robust method we demonstrated that the relative proportion of microbial subgroups in the air remained constant in different seasons, with lower concentrations of airborne microbiota in the autumn. Caves as simplified natural systems demonstrated complex relationships between atmospheric parameters and microorganisms. Bats introduce into caves varying, but not negligible, concentrations of microbes on their fur. Caves with guano had relative high concentration of airborne microbes that may represent a biohazard for animals and humans.