Prunus divaricata and Prunus armeniaca are important wild fruit trees that grow in part of the Western Tianshan Mountains in Central Asia, and they have been listed as endangered species in China. Shot-hole disease of stone fruits has become a major threat in the wild-fruit forest of the Western Tianshan Mountains. Twenty-five isolates were selected from diseased P. divaricata and P. armeniaca. According to the morphological characteristics of the culture, the 25 isolates were divided into eight morphological groups. Conidia were spindle-shaped, with ovate apical cells and truncated basal cells, with the majority of conidia comprising 3–4 septa, and the conidia had the same shape and color in morphological groups. Based on morphological and cultural characteristics and multilocus analysis using the internal transcribed spacer (ITS) region, partial large subunit (LSU) nuclear ribosomal RNA (nrRNA) gene, and the translation elongation factor 1-alpha (tef1) gene, the fungus was identified as Wilsonomyces carpophilus. The 25 W. carpophilus isolates had high genetic diversity in phylogenetic analysis, and the morphological groups did not correspond to phylogenetic groups. The pathogenicity of all W. carpophilus isolates was confirmed by inoculating healthy P. divaricata and P. armeniaca leaves and fruits. The pathogen was re-isolated from all inoculated tissues, thereby fulfilling Koch’s postulates. There were no significant differences in the pathogenicity of different isolates inoculated on P. armeniaca and P. divaricata leaves (p > 0.05). On fruit, G053 7m3 and G052 5m2 showed significant differences in inoculation on P. armeniaca, and G010 5m2 showed extremely significant differences with G004 7m2 and G004 5m2 on P. divaricata (p < 0.05). This is the first report on shot-hole disease of P. armeniaca (wild apricot) leaves and P. divaricata induced by W. carpophilus in China.

Juglans regia L. is an important and scarce natural resource that grows in the part of the western Tianshan Mountains and the Pamir Alai Mountains in Central Asia. They only distribute in Gongliu County, Yili, Xinjiang Uygur Autonomous Region in China. However, the healthy growth of J. regia was seriously affected by a fungal disease affecting leaves, branches and fruit in 2016. Sixty isolates were obtained from diseased branches, leaves and fruit collected. The pathogenicity of the isolates was confirmed by inoculating shoots and fruit collected from healthy J. regia in Gongliu County and by inoculating the leaves of J. regia seedlings. The pathogen was re‐isolated from all inoculated shoots, leaves and fruits, thereby fulfilling Koch's postulates. Furthermore, isolates from leaves were able to infect fruit and shoots and vice versa. The isolate 1429‐1 was more pathogenic to the branches than HG and HY, no significant difference between the other isolates from leaves and fruits. Based on morphological, cultural characteristics and multilocus analyses using the internal transcribed spacer region, the RNA polymerase II subunit 2 gene, the calmodulin gene, the guanine nucleotide‐binding protein subunit beta gene, the translation elongation factor 1‐alpha gene and the β‐tubulin gene sequences, the fungus was identified as Juglanconis juglandina. Although J. juglandina has been reported previously as the causal agent of stem disease, this is the first description of J. juglandina as the causal agent of a leaf and fruit disease of J. regia.