Abstract: Revealing the phylogenetic relationship between Xinjiang wild apple（Malus sieversii Roem.）and Chinese apple（Malus × domestica subsp. chinensis Li.）at molecular level would help identify the origin and taxonomy of Chinese apple，and provide theoretical basis for preserving and utilizing wild  apple resources. The sequence of ribosomal DNA internal transcribed spacers（ITS）and the coding region of the matK gene were sequenced from 52 accessions of Xinjiang wild apple，nine cultivars of Chinese apple，and one accession of M. sylvestris. Sequences of ITS and matK of 11 cultivars of Malus × domestica，14 accessions of Malus sieversii，26 of other Malus spp.，and one of Pyrus communis were retrieved from GenBank. The MEGA software（ver. 4.0）was used to analyze the divergences，variable sites，parsim-informative sites，the ratio of transition to transversion（R）and pairwise distances. The phylogenetic analysis was conducted by Maximum parsimony（MP）and Neighbor-joining（NJ）methods. The results showed that the size of ITS sequences of Xinjiang wild apple and Chinese apple ranged from 589 bp to 594 bp containing 148 parsim-informative sites with R of 1.029，whereas their matK sequences varied from 1 451 bp to 1 461 bp encompassing 16 parsim-informative sites with R of 1.442. Duplication Ⅱ was not found in the Xinjiang wild apple and Chinese apple accessions. Phylogenetic trees of ITS showed that Chinese apple，the Xinjiang wild apple（from Xinjiang，China），and M. sieversii（from GenBank）fallen into a large clade. The systematic evolution of Xinjiang wild apple appeared to occur in a geographical order of Xinyuan，Gongliu，Huocheng，and Tacheng. The matK cladograms grouped Chinese apple and the Xinjiang wild apple into one large clade with weak bootstrap support. These results indicated that Chinese apple was domesticated from Xinjiang wild apple and the matK gene was not applicable for phylogenetic analysis in intra-species of Malus × domestica. apple resources. The sequence of ribosomal DNA internal transcribed spacers（ITS）and the coding region of the matK gene were sequenced from 52 accessions of Xinjiang wild apple，nine cultivars of Chinese apple，and one accession of M. sylvestris. Sequences of ITS and matK of 11 cultivars of Malus × domestica，14 accessions of Malus sieversii，26 of other Malus spp.，and one of Pyrus communis were retrieved from GenBank. The MEGA software（ver. 4.0）was used to analyze the divergences，variable sites，parsim-informative sites，the ratio of transition to transversion（R）and pairwise distances. The phylogenetic analysis was conducted by Maximum parsimony（MP）and Neighbor-joining（NJ）methods. The results showed that the size of ITS sequences of Xinjiang wild apple and Chinese apple ranged from 589 bp to 594 bp containing 148 parsim-informative sites with R of 1.029，whereas their matK sequences varied from 1 451 bp to 1 461 bp encompassing 16 parsim-informative sites with R of 1.442. Duplication Ⅱ was not found in the Xinjiang wild apple and Chinese apple accessions. Phylogenetic trees of ITS showed that Chinese apple，the Xinjiang wild apple（from Xinjiang，China），and M. sieversii（from GenBank）fallen into a large clade. The systematic evolution of Xinjiang wild apple appeared to occur in a geographical order of Xinyuan，Gongliu，Huocheng，and Tacheng. The matK cladograms grouped Chinese apple and the Xinjiang wild apple into one large clade with weak bootstrap support. These results indicated that Chinese apple was domesticated from Xinjiang wild apple and the matK gene was not applicable for phylogenetic analysis in intra-species of Malus × domestica.

Key words: Malus ×, domestica Borkh., Malus sieversii（Ledeb.）Roem., Malus ×, domestica subsp. chinensis Li Y. N., ITS, matK, phylogenetic analysis