Abstract: Allozymic variation and genetic diversity were evaluated among nine wild and two cultivated populations of Malus hupehensis using isoelectric focusing in thin layer polyacrylamide slab gels. Twentynine loci of 12 enzyme systems were detected and used for population genetic analysis, revealing that the distribution of allele frequencies of 25 loci were significant at P ≤0.01.Nineteen locally rare alleles were found in 10 populations sampled in the study. Of 29 loci, 11 (37.9%) were duplicate loci. A high level of genetic diversity was detected in M. hupehensis , with mean number of alleles per locus A =2.127, percentage of polymorphic loci P =74.927, and mean expected heterozygosity H_e =0.376. The relative magnitude of differentiation among populations is significantly higher than those of other long lived woody plants ( G_ST =0.224). Compared with other Malus spp., this species has a moderate level of genetic variability. Gene flow among populations is only N_m =0.866, suggesting that gene drift plays an important role in influencing genetic variation and determining genetic structure.