Objective To identify the pathogens causing almond valsa canker in Xinjiang, and provide theoretical basis for disease pathogenesis analysis, the prevention and control of almond valsa canker.

Methods The diseased branches of almond germplasm resources were used as experimental materials, The pathogens were identified through pathogen isolation, pathogenicity detection, culture characteristics, morphological characteristics of fruiting bodies and phylogenetic analysis.

Results The results showed that strain 82-BT was identified as pathogenic bacteria based on Koch’s rule; Colony and morphological characteristics of fruiting bodies were consistent with Cytospora chrysosperma; According to ITS, RPB2 and EF-1α sequences, the phylogenetic trees were constructed by Bayesian approach and maximum likelihood method (ML) and Bayesian inference (BI), Topological structures are consistently in phylogenetic trees using two methods, strain 82-BT and Valsa sordida were clustered into one group with the higher support rate of 100% (ML)/1.00 (BI).

Conclusion Xinjiang almond valsa canker caused by Cytospora chrysosperma, the pathogen should be focused on controlling and researching in production.