Pollen morphology of 25 local varieties, 10 wild species, 3 cultivars and 2 hybrids of Malus were observed through scanning electron microscope, cluster analysis with UPGMA based on the shape, the length of equatorial axis, the length of polar axis and the other 8 indexes. The results indicated that Malus pollen belonged to the N3P4C5 type, prolate sphericity or ultra prolate sphericity with striate pattern and some small pores on the exine surface, the size and exine sculpture of pollen from different varieties were significantly distinct, the local variety ‘Zaobaihaitang’ which didn’t have stripe was different from others. From the UPGMA cluster analysis at the 1.30 level of genetic distance, 40 taxa could be classified into 9 groups, some local varieties distributed over the wild species, cultivates and hybrids, the others clustered into a category respectively. Pollen morphology of local varieties were rich in diversity, it need to be combined with other classification methods to taxonomy the local varieties except for some specific local varieties; and some local varieties originated from M.sieversii (Ledeb.)Roem or originated from the natural hybridization between M.sieversii (Ledeb.)Roem and others wild species or cultivars, other local varieties and the diversity emerged after natural hybrid and artificial selection, and the local varieties have important value in scientific research.