Abstract: Habitat fragmentation has complex genetic effects on plant populations. Malus sieversii exists in a few small fragmented subpopulations within a geographical population. For this study,we chose the geographical population of Gongliu,which has a high level of genetic diversity. The genotypes of 101 individuals from five subpopulations were marked using SSR loci. By analyzing the difference in genetic diversity and the genetic relationships among these five subpopulations,we aimed to investigate the effect of habitat fragmentation on the population genetic structure of [WTBX]Malus sieversii. The results showed that different levels of genetic diversity existed among these five subpopulations,in which a high level of genetic diversity was shown in marginal subpopulations of Saha and Xiaomoheer 2. These five subpopulations were clustered into two genetic lineages,which displayed an eastwest split due to the effect of geographical isolation. It is proposed that these marginal subpopulations and different genetic lineages should be considered during the processing of germplasm resource protection and the core collection of germplasm for M.sieversii.

Key words: Malus sieversii, habitat fragmentation, germplasm resource, genetic structure, marginal subpopulations, geographical isolation, Gongliu County, Xinjiang