In this study, phenolic compounds and their antioxidant activity in the pollen of anemophilous Betula and Pinus were determined. Spectrophotometric, high-performance thin-layer and liquid chromatography methods were applied. Free phenolic compounds (free PC) and phenolic compounds bound to the cell wall (bound PC) were analysed in the pollen extracts. Regardless of the pollen species, their content was 20% higher than that in bound PC extracts. Pinus pollen extracts contained 2.5 times less phenolic compounds compared to Betula. Free PC extraction from the deeper layers of Pinus pollen was minimal; the same content of phenolic compounds was obtained in both types of extracts. The bioactivity of pollen (p < 0.05) is related to the content of phenolic compounds and flavonoids in Betula free PC and in bound PC, and only in free PC extracts of Pinus. Rutin, chlorogenic and trans-ferulic acids were characterised by antioxidant activity. Phenolic acids accounted for 70–94%, while rutin constituted 2–3% of the total amount in the extracts. One of the dominant phenolic acids was trans-ferulic acid in all the Betula and Pinus samples. The specific compounds were vanillic and chlorogenic acids of Betula pollen extracts, while Pinus extracts contained gallic acid. The data obtained for the phenolic profiles and antioxidant activity of Betula and Pinus pollen can be useful for modelling food chains in ecosystems.