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Malus sieversii, a valuable crop in Xinjiang, China, is an important natural resource for researching the genetic diversity and phylogenetic evolution of the genus Malusworldwide. Samples from 152 M. sieversiiindividuals with different symptom grades of deadwood were collected from Gongliu and Xinyuan and analysed with 21 pairs of simple sequence repeat (SSR) primers, revealing molecular genetic characteristics and phylogeny of different groups and individuals. The samples showed high genetic diversity at the species level (Na= 10.76, Ne= 4.37, H= 0.73, I= 1.65, Ho= 0.71, and He= 0.73). Variation was mainly found within groups with lower genetic differentiation (Fst= 0.092) and higher gene flow (Nm= 2.67). A total of 226 alleles were obtained, of which 25 exclusive alleles were from samples with < 40% deadwood rate, and 23 exclusive alleles were from samples with > 40% deadwood rate. Specific bands relating to individuals with deadwood rate < 10% (10 exclusive alleles) or > 60% (7 exclusive alleles) were amplified with 11 pairs of SSR primers. The number of exclusive alleles from M. sieversiiplants collected in Gongliu was 52 and from those collected in Xinyuan was 24. Using unweighted pair-group method with arithmetic cluster analysis, the groups with different symptom grades from different sampling sites were shown to be clearly differentiated and formed several discrete subclades. Significantly, the six groups from Gongliu were further classified into two subclusters: Gongliu 1, including three groups with < 40% deadwood rate, and Gongliu 2, including three groups with > 40% deadwood rate.