We have used atomic force microscopy and scanning tunnelling microscopy to extract new information about the substructure of theAlnus, Betula, Fagus, LycopodiumandRhododendronpollen grain exine. Our scans of exines using atomic force microscopy and scanning tunnelling microscopy reveal somewhat similar substructures forLycopodiumspores and pollen ofAlnus, Betula, FagusandRhododendron. They show various levels of alignment and clustering of substructure components. Except forAlnus, which showed polygonal clustering of spheroids and weak alignment, there is pronounced alignment of helical units. InBetula, Fagus, LycopodiumandRhododendronthe subunits appear to be helical or perhaps consisting of elongated spheroids, these spheroids are however arranged in a way that suggest that they are part of a helical structure. The diameter of these helical subunits range from 10–15 nm inFagus, 20–25 nm inLycopodium, 35–90 nm inRhododendronup to 70–120 nm inBetula. Our preparations graded from intact or fractured fresh pollen to pollen that was acetolyzed, chemically fixed and epoxy resin embedded. While our knowledge of the exact radial/lateral orientation of most of our scans is less than perfect there were in all cases substructures or cross connections of exine units. We found results from scanning and transmission electron microscopy to be helpful in understanding images from Atomic Force- and Scanning Tunnelling Microscopy.