The aim of this study is to determine and compare microbiological contamination of anemophilous pollens (Betula verrucosa Ehrh., Betula verrucosa Ehrh. 'Youngii', Pinus sylvestris L., Pinus nigra Arnold, Pinus mugo Turra, Pinus armandii Franch., Pinus wallichiana A.B. Jacks) after collection and after not long-term storage. Samples were picked by hands aseptically in the territory of the same environmental conditions in Slovakia. Colonies of mesophilic aerobic and anaerobic bacteria, lactobacilli, total coliforms, fungi and yeast were found on pollen samples by dilution plating method. It was found significant differences in content of lactobacilli for birch pollens and fungi and yeast on pine pollens, depending on the stages – collection and storage. The microbiological quality of Betula pollen is better than Pinus pollen after collection and storage. Species factor affects the microbiota of anemophilous pollen.