In order to investigate the genetic diversity of Lilium pumilum populations in terms of palynology, the pollen morphology of 25 populations of L. pumilum were observed with the scanning electron microscope, the results showed that the pollen grain of L. pumilum was single, nearly elliptic in shape, with one germination groove on its surface. There are different degrees of difference existed among pollen morphology of 25 populations on size, mesh diameter, germination furrow width, P/E and exine ornamentation, and variability coefficient of pollen traits within populations was greater than that among populations, the maximum variation coefficient of 25.52%.