Abstract:In order to detect the population genetic diversity of apple valsa canker pathogen (Valsa mali) at the molecular level, the orthogonal designed experiments were employed to screen the optimal inter-simple sequence repeat (ISSR) amplification protocol at three levels of four factors. Eleven ISSR primers which can amplify more polymorphic loci were screened from 47 ISSR primers. Eighty seven isolates of V.mali isolated from Shaanxi Province were studied for the genetic diversity. The results showed that 129 loci were detected of which 119 loci were polymorphic, the polymorphic loci percentage was 92.25%. The POPGENE analysis results showed that the genetic diversity of V.mali groups in Shaanxi was abundant, the coefficient of population genetic differentiation (Gst) among geographical groups was 0.109, while it reached 0.891 within the populations. The genetic diversity within the populations was much more abundant than among the groups. The number of migrants per generation between two geographical groups was 2.046, which indicated that genetic information exchange was frequent between the two groups. The dendrogram based on ISSR markers revealed that the 21 natural populations were clustered into 9 clusters at the threshold of genetic similar coefficient 0.88. There was no significant correlation between the genetic relationships and their geographical originals.