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In the present study, we presented the complete mitochondrial genome (mitogenome) of Ilyonectria sp. The complete mitogenome of Ilypnectria sp. was composed of circular DNA molecules, with a total length of 34, 584 bp. The base composition of this mitogenome is as follows: A (35.31%), T (35.92%), G (15.93%), and C (12.83%). The mitogenome contains 18 protein-coding genes, 2 ribosomal RNA genes (rRNA), and 25 transfer RNA (tRNA) genes. The taxonomic status of the Ilyonectria sp. mitogenome exhibits a closest relationship with Ilyonectria destructans.