Abstract: In this study，the specific-locus amplified fragment sequencing（SLAF-seq）was used to sequence 509 accessions of Malus Mill.，and 586 454 SLAF tags were obtained，including 463 612 polymorphic SLAF tags. After sequence alignment analysis，46 460 polymorphic single nucleotide（SNP）loci were screened out according to the filter with integrity > 0.94 and minor allele frequency（MAF）> 0.05. Based on these SNP loci，phylogenetic trees among different species of Malus Mill. were constructed and principal component analysis was done. The results showed that high-throughput SNP markers could be rapidly developed in the whole genome by SLAF-seq technology，and could be directly used in the genetic diversity research of apple germplasm resources. Thirty-four species of 509 apple accessions of Malus Mill. had high levels of diversity. Among groups with more than one accession，M. toringoides had the highest level of genetic diversity，and M. × domestica subsp. chinensis had the lowest level of genetic diversity. The results of cluster analysis and principal component analysis showed that the tested accessions of Malus Mill. were divided into 5 basic groups，the groupⅠwas M. baccata，the groupⅡwas wild species of Malus Mill.，the group Ⅲ was a cluster of apple cultivars，the group Ⅳ mainly contained M. × domestica subsp. chinensis，M. robusta，M. asiatica，M. prunifolia and M. spectabilis，and the groupⅤwas M. sieversii. M. rockii，M. komarovii，M. kansuensis，M. toringoides，M. transitoria，M. yunnanensis and M. ombrophila were clustered together. The relationships among cultivated species of Malus Mill. were relatively closer. Cultivars got together with M. orientalis，M. sylveseris and some other wild species. And the relationship between M. sieversii and the cultivated species of Malus Mill. in China needed further study. The results provided a reference for further study on the classification，origin and evolution of apple germplasm resources，and provided a basis for further collection and protection.

Key words: Malus, SLAF-seq, SNP, genetic diversity