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Fungal species in the genus Trichoderma are widely used for industrial enzyme production and as biocontrol agents. In this study, we report the complete mitochondrial genome of a marine-derived Trichoderma simmonsii strain GH-Sj1, which belongs to the Harzianum clade of Trichoderma. GH-Sj1 was isolated from an edible sea alga Saccharina japonica collected from the southern coast of Korea. This newly assembled circular molecule is 28,668 bp in length and consists of 15 protein-coding genes, 26 transfer RNA genes, and two ribosomal RNA genes. Phylogenetic analysis using the maximum likelihood method shows that T. simmonsii GH-Sj1 is closely related to Trichoderma harzianum and Trichoderma lixii. To the best of our knowledge, this is the first characterization of a marine-derived mitogenome within the genus Trichoderma.