IntroductionFungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns.MethodsThe complete mitochondrial genome sequence of the mycoparasitic fungusTrichoderma koningiopsiswas determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project ofT. koningiopsisgenome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes.ResultsT. koningiopsisstrain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such asatp6,atp8,atp9,cox1,cox2,cox3,cob,nad1,nad2,nad3,nad4,nad4L,nad5, andnad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in theT. koningiopsisPOS7 mitogenome, one of them incox3 gene and the other inrnlgene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes ofT. koningiopsisstrain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina.T. koningiopsisstrain POS7 was clustered together with other representatives ofTrichodermalineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers.DiscussionThe mitochondrial genome ofT. koningiopsisPOS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.