Abstract: This study used fluorescent SSR molecular marker to analyze the genetic diversity and genetic structure of 17 populations of Malus baccata and Malus prunifolia from nine provinces. The results showed that 416 polymorphic alleles were amplified by 19 SSR primers，the percentage of polymorphic bands was 100%. The genetic diversity of overall 17 populations was high（Ne = 9.284，He = 0.862，I = 2.432），while at population level the genetic diversity of Malus prunifolia（He = 0.870，I = 2.412，Ne = 9.019）was higher than that of Malus baccata（He = 0.848，I = 2.350，Ne = 8.652）. The analysis of molecular variance（AMOVA）revealed the genetic differentiation mainly within populations（95%）.The genetic differentiation coefficient（Fst）among populations was 0.278，and gene flow（Nm）was 5.031. These results indicated that Malus baccata and Malus prunifolia were all hybrid groups by outcrossing，and there might have been genetic communication among groups at some time in the past，but at the same time they had resisted genetic differentiation among groups due to gene drift. Neighbour-Joining clustering and Structure grouping were used to classify populations，and the genetic distance between every two populations and group affiliation were not completely related to geographical location.

Key words: Malus baccata, Malus prunifolia, fluorescent SSR, genetic diversity, genetic structure