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In this study, the complete mitochondrial (mt) genomes of  Chrysoporthe austroafricana  (190,834 bp),  C .  cubensis  (89,084 bp)  and C .  deuterocubensis  (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the  Cryphonectriaceae , namely  Cryphonectria parasitica  (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the  Cryphonectriaceae . These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related  Chrysoporthe  species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the  C .  austroafricana  mt genome is the second largest in the Ascomycetes thus far.

Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species