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Citrus target spot disease caused by Pseudofabraea citricarpa poses a major threat to citrus production worldwide. Here, we report a high-quality genome assembly and annotation of a strain isolated from Chongqing, China. We have provided valuable insights into the evolution and pathogenicity of this fungus. The genome of P. citricarpa spans 44,005,176 bp with a G+C content of 44.71%, and its coding genes have been extensively annotated in various databases, such as GO and KEGG. Notably, we have predicted important proteins, such as secreted proteins, transmembrane proteins, and carbohydrate-active enzymes. Our findings serve as a key resource for understanding the global spread of this pathogen, enabling better control measures to be implemented. In conclusion, this study enriches our understanding of P. citricarpa and provides a foundation for future research in the field. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.