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Usnea is a genus of lichenized Ascomycete that grows in moist mountain areas. It is a food for wild animals and can also be used as medicine. We describe the complete mitochondrial genome of the lichenized fungi Usnea jiangxiensis. It is a circular molecule of 62,531 bp in size, and all genes show the typical gene arrangement conforming to the mold consensus. The mitochondrial genome sequence of U. jiangxiensis and other eight species were used for phylogenetic analysis by the maximum likelihood method. Phylogenetic analysis demonstrated that U. jiangxiensis most closely related to U. ceratina. The complete chloroplast genomes of U. jiangxiensis would be useful for future investigation of genetics, evolution and clinical identification of Usnea species. [ABSTRACT FROM AUTHOR]