Fungal mitochondrial genomes are good reservoir of group I and group II introns and intron-encoded proteins (IEPs). Those catalytic introns (ribozymes) and their IEPs have application in biotechnology and have contribution in the mitochondrial genome evolution. We have sequenced mitochondrial genomes of four strains of Endoconidiophora resinifera collected from Europe and North America. Those mitochondrial genomes are among the largest ones of the fungal kingdom having the largest cox1 gene reported so far. The study revealed that the gene or genome size expansion is mainly influenced by the number of intron. An updated model of the mobility mechanism of introns and IEPs was also proposed. An intron landscape was constructed by collecting and aligning nad5 genes from Ascomycota and Basidiomycota to find out the intron homing sites and intron distribution among the fungal species.