Abstract: Pollen morphologies of 12 lily species (including 4 wild and 8 cultivated species) were examined by scanning electron microscopy (SEM). The pollen shapes of 4 wild (Lilium pumilum, L. davidi, L. lancifolium and L. leichtlinii var. maximowiczii) and 4 cultivated (Brunello, Prato, Pollyanna and Red knight) lily species were elliptic balls, while those of the other four cultivars (Algarve, Yelloween, Samur and Siberia) were a long ellipsoid. Most mesh ridges of the pollen from the 12 species were composed of particles or tumors and their width ranged from 1.20 to 2.78 μm. The shapes of pollen mesh are mostly irregular polygons to nearly round with sizes from 2.11 to 7.66 μm. The surface ornamentation of L. leichtlinii var. maximowiczii and Red knight pollens showed the coexistence of duplicolumellate and simplicolumellate, while the other 10 species were netted simplicolumellate. The forms of pollen grains were single, ellipsoidal in polar view and boat-shaped in equatorial view, with single-channel apertures the length of the ditch. Cluster analysis of pollen morphology for the 12 lily species showed that L. pumilum and L. davidi, L. lancifolium and L. leichtlinii var. maximowiczii, Algarve and Samur, Prato and Pollyanna have close genetic relationships. The 12 species can be divided into 3 groups based on cluster results.